Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 13 of 97
Found at i:6390439 original size:46 final size:48
Alignment explanation
Indices: 6390338--6390439 Score: 111
Period size: 46 Copynumber: 2.2 Consensus size: 48
6390328 ATATTTATTT
* * *
6390338 ATTTATTTTTTAAATATTAATAATTTATAATTAATTAAAATATTAATA
1 ATTTAATTTTTAAATATCAATAATTTATAATTAATTAAAATACTAATA
* * *
6390386 ATATAATTTTT-AATATCAAT-ATTT-TAATATAATTTAATTACTAATA
1 ATTTAATTTTTAAATATCAATAATTTATAAT-TAATTAAAATACTAATA
*
6390432 TTTTAATT
1 ATTTAATT
6390440 AATAATATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
45 4 0.09
46 24 0.53
47 8 0.18
48 9 0.20
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (48 bp):
ATTTAATTTTTAAATATCAATAATTTATAATTAATTAAAATACTAATA
Found at i:6390572 original size:29 final size:29
Alignment explanation
Indices: 6390515--6390572 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
6390505 TAATCATATT
*
6390515 AATATTAATAATGTTTAAATTATATATAA
1 AATATTAATAATGTTTAAATTATAAATAA
6390544 AATATTAAT-AT-TTTAAATTTTATAAATAA
1 AATATTAATAATGTTTAAA--TTATAAATAA
6390573 TTTATTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 6 0.23
28 2 0.08
29 18 0.69
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
AATATTAATAATGTTTAAATTATAAATAA
Found at i:6396592 original size:2 final size:2
Alignment explanation
Indices: 6396585--6396642 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
6396575 AAGTTGTCAA
6396585 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6396627 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
6396643 NNNNNNNNNN
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6400873 original size:3 final size:3
Alignment explanation
Indices: 6400865--6400892 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
6400855 CCTTTGATCC
6400865 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
6400893 TCGAAACCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:6421909 original size:36 final size:36
Alignment explanation
Indices: 6421869--6421959 Score: 101
Period size: 27 Copynumber: 2.8 Consensus size: 36
6421859 TCAACTCTAC
*
6421869 CAACTCTCTGTTGAGCACCATCGTCATCAGCTCTTT
1 CAACTCTCTGTTGAGCACCATCGTCATCAGCTCTGT
*
6421905 CAACTCTC---TGA--A-C-T-GT-ATGAGCTCTGT
1 CAACTCTCTGTTGAGCACCATCGTCATCAGCTCTGT
6421932 CAACTCTCTGTTGAGCACCATCGTCATC
1 CAACTCTCTGTTGAGCACCATCGTCATC
6421960 GGGCTGTGGT
Statistics
Matches: 43, Mismatches: 3, Indels: 18
0.67 0.05 0.28
Matches are distributed among these distances:
27 17 0.40
28 2 0.05
29 1 0.02
30 4 0.09
31 1 0.02
32 1 0.02
33 4 0.09
34 1 0.02
35 2 0.05
36 10 0.23
ACGTcount: A:0.21, C:0.32, G:0.15, T:0.32
Consensus pattern (36 bp):
CAACTCTCTGTTGAGCACCATCGTCATCAGCTCTGT
Found at i:6421912 original size:63 final size:63
Alignment explanation
Indices: 6421836--6421959 Score: 194
Period size: 63 Copynumber: 2.0 Consensus size: 63
6421826 GATCATCTTT
* *
6421836 CTCTTTCAACTCTCTGAATTGTCTCAACTCTACCAACTCTCTGTTGAGCACCATCGTCATCAG
1 CTCTTTCAACTCTCTGAACTGTATCAACTCTACCAACTCTCTGTTGAGCACCATCGTCATCAG
* * **
6421899 CTCTTTCAACTCTCTGAACTGTATGAGCTCTGTCAACTCTCTGTTGAGCACCATCGTCATC
1 CTCTTTCAACTCTCTGAACTGTATCAACTCTACCAACTCTCTGTTGAGCACCATCGTCATC
6421960 GGGCTGTGGT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.34
Consensus pattern (63 bp):
CTCTTTCAACTCTCTGAACTGTATCAACTCTACCAACTCTCTGTTGAGCACCATCGTCATCAG
Found at i:6422249 original size:31 final size:31
Alignment explanation
Indices: 6422225--6422495 Score: 416
Period size: 31 Copynumber: 8.7 Consensus size: 31
6422215 GTTATAACAC
6422225 TTTACGTTATATGCATGGTGTGTTACCACAT
1 TTTACGTTATATGCATGGTGTGTTACCACAT
*
6422256 TTTACGTTATATGCATGGTGTGTTACAACAT
1 TTTACGTTATATGCATGGTGTGTTACCACAT
* *
6422287 TTTACGTTATATGTATGGTGTGTTACAACAT
1 TTTACGTTATATGCATGGTGTGTTACCACAT
*
6422318 TTTACGTTATATGCATGGTGTGTTACCATAT
1 TTTACGTTATATGCATGGTGTGTTACCACAT
*
6422349 TTTACGTTATATGCATGGTGTGTTATCACAT
1 TTTACGTTATATGCATGGTGTGTTACCACAT
** *
6422380 TTTACGTTATATATATGGCGTGTTACCACAT
1 TTTACGTTATATGCATGGTGTGTTACCACAT
**
6422411 TTTATATTATATGCATGGTGTGTTACCACAT
1 TTTACGTTATATGCATGGTGTGTTACCACAT
** *
6422442 TTTATATTATATGTATGGTGTGTTACCACAT
1 TTTACGTTATATGCATGGTGTGTTACCACAT
*
6422473 TTTACGTTATATGCATGGCGTGT
1 TTTACGTTATATGCATGGTGTGT
6422496 AACAACATGA
Statistics
Matches: 219, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 219 1.00
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (31 bp):
TTTACGTTATATGCATGGTGTGTTACCACAT
Found at i:6426718 original size:86 final size:86
Alignment explanation
Indices: 6426046--6426709 Score: 835
Period size: 86 Copynumber: 7.7 Consensus size: 86
6426036 GAGCAGATGC
* * * ** * * *
6426046 TTGTGGTGACATGTTGAGTGCACACAAACTTATGGCGTGACACGTTAACTTGTTGCAGTCTTGTG
1 TTGTGGTGACACGCTGAGTGAATGCAGACTTATGGCGTGACACGCTGACTTGTTGCAGTCTTGTG
*
6426111 GGGTGACACGGCACGGGCCAA
66 GGGTGACACAGCACGGGCCAA
* * *
6426132 TTGTGGTGACACGTTGAGTGAATGCAGACTTCTGACGTGACACGCTGACTTGTTGCAGTCTTGTG
1 TTGTGGTGACACGCTGAGTGAATGCAGACTTATGGCGTGACACGCTGACTTGTTGCAGTCTTGTG
* *
6426197 GGGTGACACACCACGGCCCAA
66 GGGTGACACAGCACGGGCCAA
* * *
6426218 TTGTGGTGACACGCTGAGTGCATGCAGACTTATGGCGTGACACGCTGACTTGTTACAATCTTGTG
1 TTGTGGTGACACGCTGAGTGAATGCAGACTTATGGCGTGACACGCTGACTTGTTGCAGTCTTGTG
* * * *
6426283 AGATAACACAACACGGGCCAA
66 GGGTGACACAGCACGGGCCAA
* * * *
6426304 TTGTGGTGACACGCTAAGTGAATGTAGACTTATGACGTGACACGCTGACTTGTTGTAGTCTTGTG
1 TTGTGGTGACACGCTGAGTGAATGCAGACTTATGGCGTGACACGCTGACTTGTTGCAGTCTTGTG
*
6426369 GGGTGACACGGCACGGGCCAA
66 GGGTGACACAGCACGGGCCAA
* * * * * * **
6426390 TTGTGGTGAGATGCTGAGTGAATGTAGACTTATGGAGTGACACGTTAACTTGTTGCAGTCTTGCA
1 TTGTGGTGACACGCTGAGTGAATGCAGACTTATGGCGTGACACGCTGACTTGTTGCAGTCTTGTG
*
6426455 GGGTGACACTA-CATGGGCCAA
66 GGGTGACAC-AGCACGGGCCAA
* * * * * * * *
6426476 TTGTGGTGAGATGTTGAGTGTATGCAGACTTCTGGCATGACACGCTGACTTGTTGAAGTCTTATG
1 TTGTGGTGACACGCTGAGTGAATGCAGACTTATGGCGTGACACGCTGACTTGTTGCAGTCTTGTG
* *
6426541 GGGTGACACGGCACGAGCCAA
66 GGGTGACACAGCACGGGCCAA
* * **
6426562 TTGTGGTGATACACTGAGTGAATGCAGACTTATGGCGTGACACGCTGACTTGTTATAGTCTTGTG
1 TTGTGGTGACACGCTGAGTGAATGCAGACTTATGGCGTGACACGCTGACTTGTTGCAGTCTTGTG
*
6426627 GGGTGACACAGCACGAGCCAA
66 GGGTGACACAGCACGGGCCAA
* **
6426648 TTGTGGTGACACGCTGAGTGAATGCAAACTTATGGTATGACACGCTGACTTGTTGCAGTCTT
1 TTGTGGTGACACGCTGAGTGAATGCAGACTTATGGCGTGACACGCTGACTTGTTGCAGTCTT
6426710 ATAAGGTGAT
Statistics
Matches: 496, Mismatches: 80, Indels: 4
0.86 0.14 0.01
Matches are distributed among these distances:
86 496 1.00
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.27
Consensus pattern (86 bp):
TTGTGGTGACACGCTGAGTGAATGCAGACTTATGGCGTGACACGCTGACTTGTTGCAGTCTTGTG
GGGTGACACAGCACGGGCCAA
Found at i:6428228 original size:81 final size:81
Alignment explanation
Indices: 6428123--6428652 Score: 573
Period size: 81 Copynumber: 6.5 Consensus size: 81
6428113 AGGAAGAGCT
* * **
6428123 CTCCTTCAACCACGAGCGACTGAAGGTCCCCTTCCCCTCTTGCAGATGCATCGATAACCAGATCA
1 CTCCTTCAGCCACGAGCGAGTGAAGGTCCCCTTCCCCTCCCGCAGATGCATCGATAACCAGATCA
6428188 GCCTCAAGAACATGGA
66 GCCTCAAGAACATGGA
* * *
6428204 CTCCTTCAGCCACGAGTGAGTGAAGGTCCCC-TCCCCTTCCCGCAAATACATCGATAACC-GAAT
1 CTCCTTCAGCCACGAGCGAGTGAAGGTCCCCTTCCCC-TCCCGCAGATGCATCGATAACCAG-AT
6428267 CAGCCTCAAGAACATGGA
64 CAGCCTCAAGAACATGGA
* * * * * *
6428285 CTCTTTCAGCCACGAGAGAGTAAAGGTCCCTTTCCCCTCCCACAGATGCATCGATAATCAGATCA
1 CTCCTTCAGCCACGAGCGAGTGAAGGTCCCCTTCCCCTCCCGCAGATGCATCGATAACCAGATCA
*
6428350 ACCTC-AGAAACATGGA
66 GCCTCAAG-AACATGGA
* * * ** * * *
6428366 CTCTTTCAGCCATGAGCAAGTGAAGGTCCCCTTTTCTTCCCGCAGATGCATCGATAACTAAATCA
1 CTCCTTCAGCCACGAGCGAGTGAAGGTCCCCTTCCCCTCCCGCAGATGCATCGATAACCAGATCA
* *
6428431 GCCTTAAGAATATGGA
66 GCCTCAAGAACATGGA
* * * * * **
6428447 TTACTTCAGTCACGAGTGAGTGAAGGTCCCCCTCCCCTCCCATAGATGCATCGATAACCAGATCA
1 CTCCTTCAGCCACGAGCGAGTGAAGGTCCCCTTCCCCTCCCGCAGATGCATCGATAACCAGATCA
6428512 GCCTCAAGAACATGGA
66 GCCTCAAGAACATGGA
** * * * * * * * *
6428528 CTTTTTTAGCCATGAGCGAGTGAAGGTCCCTTTTCCTTCCCCCAAATGCATCGATAA-CTGAATC
1 CTCCTTCAGCCACGAGCGAGTGAAGGTCCCCTTCCCCTCCCGCAGATGCATCGATAACCAG-ATC
* *
6428592 AGCCTTAAGAATATGGA
65 AGCCTCAAGAACATGGA
* * * *
6428609 TTCCTTCAGCCACGAACGAGTGAAGGTCCCTTTCCCCTCTCGCA
1 CTCCTTCAGCCACGAGCGAGTGAAGGTCCCCTTCCCCTCCCGCA
6428653 TCGATAACCG
Statistics
Matches: 367, Mismatches: 75, Indels: 14
0.80 0.16 0.03
Matches are distributed among these distances:
80 10 0.03
81 349 0.95
82 8 0.02
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (81 bp):
CTCCTTCAGCCACGAGCGAGTGAAGGTCCCCTTCCCCTCCCGCAGATGCATCGATAACCAGATCA
GCCTCAAGAACATGGA
Found at i:6428407 original size:162 final size:161
Alignment explanation
Indices: 6428126--6428647 Score: 681
Period size: 162 Copynumber: 3.2 Consensus size: 161
6428116 AAGAGCTCTC
* * * ***
6428126 CTTCAACCACGAGCGACTGAAGGTCCCCTTCCCCTCTTGCAGATGCATCGATAACCAGATCAGCC
1 CTTCAGCCACGAGAGAGTGAAGGTCCCCTTCCCCTCCCACAGATGCATCGATAACCAGATCAGCC
* * * *** *
6428191 TCAAGAACATGGACTCCTTCAGCCACGAGTGAGTGAAGGTCCCCTCCCCTTCCCGCAAATACATC
66 TCAAGAACATGGACTCTTTCAGCCATGAGCGAGTGAAGGTCCCCTTTTCTTCCCGCAAATGCATC
* * * *
6428256 GATAACCGAATCAGCCTCAAGAACATGGACT
131 GATAACTGAATCAGCCTTAAGAATATGGATT
* * * *
6428287 CTTTCAGCCACGAGAGAGTAAAGGTCCCTTTCCCCTCCCACAGATGCATCGATAATCAGATCAAC
1 C-TTCAGCCACGAGAGAGTGAAGGTCCCCTTCCCCTCCCACAGATGCATCGATAACCAGATCAGC
* *
6428352 CTC-AGAAACATGGACTCTTTCAGCCATGAGCAAGTGAAGGTCCCCTTTTCTTCCCGCAGATGCA
65 CTCAAG-AACATGGACTCTTTCAGCCATGAGCGAGTGAAGGTCCCCTTTTCTTCCCGCAAATGCA
*
6428416 TCGATAACTAAATCAGCCTTAAGAATATGGATT
129 TCGATAACTGAATCAGCCTTAAGAATATGGATT
* * * *
6428449 ACTTCAGTCACGAGTGAGTGAAGGTCCCCCTCCCCTCCCATAGATGCATCGATAACCAGATCAGC
1 -CTTCAGCCACGAGAGAGTGAAGGTCCCCTTCCCCTCCCACAGATGCATCGATAACCAGATCAGC
* * *
6428514 CTCAAGAACATGGACTTTTTTAGCCATGAGCGAGTGAAGGT-CCCTTTTCCTTCCCCCAAATGCA
65 CTCAAGAACATGGACTCTTTCAGCCATGAGCGAGTGAAGGTCCCCTTTT-CTTCCCGCAAATGCA
6428578 TCGATAACTGAATCAGCCTTAAGAATATGGATT
129 TCGATAACTGAATCAGCCTTAAGAATATGGATT
*
6428611 CCTTCAGCCACGA-ACGAGTGAAGGTCCCTTTCCCCTC
1 -CTTCAGCCACGAGA-GAGTGAAGGTCCCCTTCCCCTC
6428648 TCGCATCGAT
Statistics
Matches: 312, Mismatches: 43, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
161 10 0.03
162 299 0.96
163 3 0.01
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.23
Consensus pattern (161 bp):
CTTCAGCCACGAGAGAGTGAAGGTCCCCTTCCCCTCCCACAGATGCATCGATAACCAGATCAGCC
TCAAGAACATGGACTCTTTCAGCCATGAGCGAGTGAAGGTCCCCTTTTCTTCCCGCAAATGCATC
GATAACTGAATCAGCCTTAAGAATATGGATT
Found at i:6430436 original size:25 final size:25
Alignment explanation
Indices: 6430408--6430474 Score: 91
Period size: 25 Copynumber: 2.7 Consensus size: 25
6430398 TATCAAGTCA
6430408 AATGTCGTGACACGCCATACAT-AT
1 AATGTCGTGACACGCCATACATAAT
*
6430432 CAATGTCGTGACACGCCATGCATAAT
1 -AATGTCGTGACACGCCATACATAAT
* *
6430458 AGTGTCGTGACATGCCA
1 AATGTCGTGACACGCCA
6430475 ATCATTGTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 36 0.95
26 2 0.05
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (25 bp):
AATGTCGTGACACGCCATACATAAT
Found at i:6430615 original size:55 final size:55
Alignment explanation
Indices: 6430510--6431149 Score: 656
Period size: 55 Copynumber: 11.8 Consensus size: 55
6430500 ACTAACAGCT
* * *
6430510 GTGACACGTTAAAAACAC-AAAAT-CAATTAACCCACAACATGCCAGGAACAACC
1 GTGACACGCTAAAAACCCAAAAATCCAATTAACCCACAACACGCCAGGAACAACC
* * * *
6430563 GTGACACGCTAAAAACCCAAAAATCTAGTTAACCCACAATACGTCAGGAACAACC
1 GTGACACGCTAAAAACCCAAAAATCCAATTAACCCACAACACGCCAGGAACAACC
*** * *
6430618 GTGACACGCTAAAAACCCAAAAAAT-CAATTAACCCACAACACTTTAGGAACAGCA
1 GTGACACGCTAAAAACCC-AAAAATCCAATTAACCCACAACACGCCAGGAACAACC
* * * *
6430673 GTGACACGCCAAAAACCAAAAAATCCAATTAACCCACTACACTCCAGGAACAACC
1 GTGACACGCTAAAAACCCAAAAATCCAATTAACCCACAACACGCCAGGAACAACC
* * * * * * * *
6430728 GTGACACACTAAAAATCCAAAAAACCAGTTAATCCACAACATGCTAGGAACAGCC
1 GTGACACGCTAAAAACCCAAAAATCCAATTAACCCACAACACGCCAGGAACAACC
* ** * ***
6430783 GTGACACG--------CCAAAAATCTAATTAACCCACAACACATCATGAACAGTT
1 GTGACACGCTAAAAACCCAAAAATCCAATTAACCCACAACACGCCAGGAACAACC
* ** * * *
6430830 GTGACACGCTGAAAATTCAAAAATCCAGTTAACCCACAACACGCCAAGAACAGCC
1 GTGACACGCTAAAAACCCAAAAATCCAATTAACCCACAACACGCCAGGAACAACC
* * * * *
6430885 GTGACACGCTAAAAACTCAAAAAACCAGTTAACCCACAACACCCCAGGAACAGCC
1 GTGACACGCTAAAAACCCAAAAATCCAATTAACCCACAACACGCCAGGAACAACC
* * *
6430940 GTAACACGTTAAAAACCCAAAAAACCAATTAACCCACAACACGCCAGGAACAACC
1 GTGACACGCTAAAAACCCAAAAATCCAATTAACCCACAACACGCCAGGAACAACC
* * *
6430995 GTGACATGCCAAAAACCCAAAAATCCAATTAACCCACAACACGCCAAGAACAACC
1 GTGACACGCTAAAAACCCAAAAATCCAATTAACCCACAACACGCCAGGAACAACC
* * * * * * *
6431050 GTGAGACGCTAAAAACCCAAAAAACCAGTTAACCCATAATACGCCAAGAACAACT
1 GTGACACGCTAAAAACCCAAAAATCCAATTAACCCACAACACGCCAGGAACAACC
* ***
6431105 GTGACACACTAAAAACCCAAAAA-CTGGTTAACCCACAACACGCCA
1 GTGACACGCTAAAAACCCAAAAATCCAATTAACCCACAACACGCCA
6431150 TATGCAAACG
Statistics
Matches: 491, Mismatches: 84, Indels: 23
0.82 0.14 0.04
Matches are distributed among these distances:
47 36 0.07
53 16 0.03
54 29 0.06
55 404 0.82
56 6 0.01
ACGTcount: A:0.45, C:0.31, G:0.11, T:0.12
Consensus pattern (55 bp):
GTGACACGCTAAAAACCCAAAAATCCAATTAACCCACAACACGCCAGGAACAACC
Found at i:6431017 original size:267 final size:266
Alignment explanation
Indices: 6430528--6431149 Score: 690
Period size: 267 Copynumber: 2.3 Consensus size: 266
6430518 TTAAAAACAC
** *
6430528 AAAATCAATTAACCCACAACATGCCAGGAACAACCGTGACACGCTAAAAACCCAAAAATCTAGTT
1 AAAATCAATTAACCCACAACACACCAGGAACAACCGTGACACGCTAAAAACCCAAAAATCCAGTT
* * * *
6430593 AACCCACAATACGTCAGGAACAACCGTGACACGCTAAAAACCCAAAAAATCAATTAACCCACAAC
66 AACCCACAACACGCCAAGAACAACCGTGACACGCTAAAAACCCAAAAAACCAATTAACCCACAAC
*** * * *
6430658 ACTTTAGGAACAGCAGTGACACGCCAAAAACCAAAAAATCCAATTAACCCACTACACTCCAGGAA
131 ACCCCAGGAACAGCAGTAACACGCCAAAAACCAAAAAATCCAATTAACCCACAACACGCCAGGAA
* * * * * * * *
6430723 CAACCGTGACACACTAAAAATCCAAAAAACCAGTTAATCCACAACATGCTAGGAACAGCCGTGAC
196 CAACCGTGACACACCAAAAACCCAAAAAACCAATTAACCCACAACACGCCAAGAACAACCGTGAC
6430788 ACGCCA
261 ACGCCA
* * *** * **
6430794 AAAATCTAATTAACCCACAACACATCATGAACAGTTGTGACACGCTGAAAATTCAAAAATCCAGT
1 AAAATC-AATTAACCCACAACACACCAGGAACAACCGTGACACGCTAAAAACCCAAAAATCCAGT
* * *
6430859 TAACCCACAACACGCCAAGAACAGCCGTGACACGCTAAAAACTCAAAAAACCAGTTAACCCACAA
65 TAACCCACAACACGCCAAGAACAACCGTGACACGCTAAAAACCCAAAAAACCAATTAACCCACAA
* **
6430924 CACCCCAGGAACAGCCGTAACACGTTAAAAACCCAAAAAA-CCAATTAACCCACAACACGCCAGG
130 CACCCCAGGAACAGCAGTAACACGCCAAAAA-CCAAAAAATCCAATTAACCCACAACACGCCAGG
** *
6430988 AACAACCGTGACATGCCAAAAACCCAAAAATCCAATTAACCCACAACACGCCAAGAACAACCGTG
194 AACAACCGTGACACACCAAAAACCCAAAAAACCAATTAACCCACAACACGCCAAGAACAACCGTG
*
6431053 AGACGCTAAAAACCCAA
259 ACACG--------CC-A
* * * * * * * * **
6431070 AAAACCAGTTAACCCATAATACGCCAAGAACAACTGTGACACACTAAAAACCCAAAAA-CTGGTT
1 AAAATCAATTAACCCACAACACACCAGGAACAACCGTGACACGCTAAAAACCCAAAAATCCAGTT
6431134 AACCCACAACACGCCA
66 AACCCACAACACGCCA
6431150 TATGCAAACG
Statistics
Matches: 291, Mismatches: 54, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
266 6 0.02
267 209 0.72
268 8 0.03
274 20 0.07
275 42 0.14
276 6 0.02
ACGTcount: A:0.45, C:0.31, G:0.11, T:0.12
Consensus pattern (266 bp):
AAAATCAATTAACCCACAACACACCAGGAACAACCGTGACACGCTAAAAACCCAAAAATCCAGTT
AACCCACAACACGCCAAGAACAACCGTGACACGCTAAAAACCCAAAAAACCAATTAACCCACAAC
ACCCCAGGAACAGCAGTAACACGCCAAAAACCAAAAAATCCAATTAACCCACAACACGCCAGGAA
CAACCGTGACACACCAAAAACCCAAAAAACCAATTAACCCACAACACGCCAAGAACAACCGTGAC
ACGCCA
Found at i:6431061 original size:165 final size:165
Alignment explanation
Indices: 6430503--6431149 Score: 731
Period size: 165 Copynumber: 4.0 Consensus size: 165
6430493 TTGTTACACT
* ** * * *
6430503 AACAGCTGTGACACGTTAAAAACAC-AAAAT-CAATTAACCCACAACATGCCAGGAACAACCGTG
1 AACAGCAGTGACACGCCAAAAACCCAAAAATCCAATTAACCCACAACACGCCAAGAACAACCGTG
* * * *
6430566 ACACGCTAAAAACCCAAAAATCTAGTTAACCCACAATACGTCAGGAACAACCGTGACACGCTAAA
66 ACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACACGCCAGGAACAACCGTGACACGCTAAA
* ***
6430631 AACCCAAAAAATCAATTAACCCACAACACTTTAGG
131 AACCCAAAAAACCAATTAACCCACAACACGCCAGG
* * * *
6430666 AACAGCAGTGACACGCCAAAAACCAAAAAATCCAATTAACCCACTACACTCCAGGAACAACCGTG
1 AACAGCAGTGACACGCCAAAAACCCAAAAATCCAATTAACCCACAACACGCCAAGAACAACCGTG
* * * * * *
6430731 ACACACTAAAAATCCAAAAAACCAGTTAATCCACAACATGCTAGGAACAGCCGTGACACG-----
66 ACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACACGCCAGGAACAACCGTGACACGCTAAA
* * ** *
6430791 ---CCAAAAATCTAATTAACCCACAACACATCATG
131 AACCCAAAAAACCAATTAACCCACAACACGCCAGG
** ** ** * *
6430823 AACAGTTGTGACACGCTGAAAATTCAAAAATCCAGTTAACCCACAACACGCCAAGAACAGCCGTG
1 AACAGCAGTGACACGCCAAAAACCCAAAAATCCAATTAACCCACAACACGCCAAGAACAACCGTG
* * * * *
6430888 ACACGCTAAAAACTCAAAAAACCAGTTAACCCACAACACCCCAGGAACAGCCGTAACACGTTAAA
66 ACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACACGCCAGGAACAACCGTGACACGCTAAA
6430953 AACCCAAAAAACCAATTAACCCACAACACGCCAGG
131 AACCCAAAAAACCAATTAACCCACAACACGCCAGG
* * *
6430988 AACAACCGTGACATGCCAAAAACCCAAAAATCCAATTAACCCACAACACGCCAAGAACAACCGTG
1 AACAGCAGTGACACGCCAAAAACCCAAAAATCCAATTAACCCACAACACGCCAAGAACAACCGTG
* * * * * *
6431053 AGACGCTAAAAACCCAAAAAACCAGTTAACCCATAATACGCCAAGAACAACTGTGACACACTAAA
66 ACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACACGCCAGGAACAACCGTGACACGCTAAA
***
6431118 AACCC-AAAAACTGGTTAACCCACAACACGCCA
131 AACCCAAAAAACCAATTAACCCACAACACGCCA
6431150 TATGCAAACG
Statistics
Matches: 401, Mismatches: 73, Indels: 19
0.81 0.15 0.04
Matches are distributed among these distances:
157 131 0.33
163 20 0.05
164 29 0.07
165 221 0.55
ACGTcount: A:0.45, C:0.31, G:0.11, T:0.13
Consensus pattern (165 bp):
AACAGCAGTGACACGCCAAAAACCCAAAAATCCAATTAACCCACAACACGCCAAGAACAACCGTG
ACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACACGCCAGGAACAACCGTGACACGCTAAA
AACCCAAAAAACCAATTAACCCACAACACGCCAGG
Found at i:6431623 original size:22 final size:23
Alignment explanation
Indices: 6431546--6431625 Score: 83
Period size: 23 Copynumber: 3.5 Consensus size: 23
6431536 TTCTTTCACA
* * *
6431546 CCATGGCGAGTCACATATTCAAC
1 CCATGGCGTGTCACATGTTCAAG
*
6431569 CCATGGCGTGTCACGTGTTCAAG
1 CCATGGCGTGTCACATGTTCAAG
* *
6431592 CCATGCCGTGTCACATG-TC-TG
1 CCATGGCGTGTCACATGTTCAAG
6431613 ACCATGGCGTGTC
1 -CCATGGCGTGTC
6431626 TCACACTCTA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
21 1 0.02
22 13 0.27
23 34 0.71
ACGTcount: A:0.20, C:0.30, G:0.25, T:0.25
Consensus pattern (23 bp):
CCATGGCGTGTCACATGTTCAAG
Found at i:6431789 original size:23 final size:23
Alignment explanation
Indices: 6431734--6431814 Score: 67
Period size: 23 Copynumber: 3.5 Consensus size: 23
6431724 CGTGTCACAC
*
6431734 CCGTGTCACACATTATCA-CTGTG
1 CCGTGTCACACATTATGACCT-TG
*
6431757 TCGT-TGCACACATTATGACCTTG
1 CCGTGT-CACACATTATGACCTTG
* * *
6431780 CCGTGTCACACGTTCTGACCATG
1 CCGTGTCACACATTATGACCTTG
* *
6431803 ACATGTCACACA
1 CCGTGTCACACA
6431815 CTCCAAACAC
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
22 1 0.02
23 42 0.91
24 3 0.07
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.28
Consensus pattern (23 bp):
CCGTGTCACACATTATGACCTTG
Found at i:6431868 original size:23 final size:23
Alignment explanation
Indices: 6431832--6431882 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
6431822 CACTGTCGTG
* *
6431832 TCACATATTCTCACCGTGCTGTC
1 TCACACATTATCACCGTGCTGTC
* *
6431855 TCACACATTATCACCTTGCTGTG
1 TCACACATTATCACCGTGCTGTC
6431878 TCACA
1 TCACA
6431883 GATTCCCTCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.22, C:0.33, G:0.12, T:0.33
Consensus pattern (23 bp):
TCACACATTATCACCGTGCTGTC
Found at i:6431985 original size:23 final size:23
Alignment explanation
Indices: 6431932--6431986 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
6431922 ATGTCAAACC
*
6431932 CGTGTCACACATTATCAATGTGT
1 CGTGTCACACATTATCAATGTAT
* * *
6431955 TGTTTCACACATTATCACCT-TAT
1 CGTGTCACACATTATCA-ATGTAT
6431978 CGTGTCACA
1 CGTGTCACA
6431987 TGTTCTGACC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.36
Consensus pattern (23 bp):
CGTGTCACACATTATCAATGTAT
Found at i:6432008 original size:104 final size:104
Alignment explanation
Indices: 6431828--6432194 Score: 389
Period size: 104 Copynumber: 3.5 Consensus size: 104
6431818 CAAACACTGT
* * * * * * *
6431828 CGTGTCACATATTCTCACCGTG-CTGTCTCACACATTATCACCTTGCTGTGTCACAGATTCCCTC
1 CGTGTCACACATTATCACCGTGTC-GTCTCACACATTATCACCCTACCGTGTCACAGATTCTCAC
* * * *
6431892 CATAGCGTGTCACACACTCTAAACCTTGTCATGTCAAACC
65 CATGGCGTGTCACACACTCTAAACATTGTCGTGTCACACC
** * * * * *
6431932 CGTGTCACACATTATCAATGTGTTGTTTCACACATTATCACCTTATCGTGTCACATG-TTCTGAC
1 CGTGTCACACATTATCACCGTGTCGTCTCACACATTATCACCCTACCGTGTCACA-GATTCTCAC
* *
6431996 CATGGCGTGTCACACATTCTAAACGTTGTCGTGTCACACC
65 CATGGCGTGTCACACACTCTAAACATTGTCGTGTCACACC
* * * * * * *
6432036 TGTGTCACATATTCTCACCATGTCGTCTCACACATTATCACCCTGCCATGTCACAGATTCCTTA-
1 CGTGTCACACATTATCACCGTGTCGTCTCACACATTATCACCCTACCGTGTCACAGATT-CTCAC
* *
6432100 CATGACGTGTCACACACTCTAAACATTGCCGTGTCACACC
65 CATGGCGTGTCACACACTCTAAACATTGTCGTGTCACACC
* * * *
6432140 TGTGTCACACATTATCACTGTGTCGTTTCACACATTATAACCCTACCGTGTCACA
1 CGTGTCACACATTATCACCGTGTCGTCTCACACATTATCACCCTACCGTGTCACA
6432195 CCCTGTTACA
Statistics
Matches: 217, Mismatches: 42, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
103 1 0.00
104 212 0.98
105 4 0.02
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.31
Consensus pattern (104 bp):
CGTGTCACACATTATCACCGTGTCGTCTCACACATTATCACCCTACCGTGTCACAGATTCTCACC
ATGGCGTGTCACACACTCTAAACATTGTCGTGTCACACC
Found at i:6432313 original size:24 final size:23
Alignment explanation
Indices: 6432241--6432318 Score: 70
Period size: 24 Copynumber: 3.3 Consensus size: 23
6432231 TCACCCTGAT
*
6432241 GTGTCACACACTCTAAACCCTGTC
1 GTGTCACA-ACTCTAAACCCTGCC
* * *
6432265 ATGTCAC-ACGTCT-GACCATGCC
1 GTGTCACAAC-TCTAAACCCTGCC
*
6432287 GTGTCACAAACTCTATACCCTGCC
1 GTGTCAC-AACTCTAAACCCTGCC
6432311 GTGTCACA
1 GTGTCACA
6432319 CCCGTCTCAT
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
22 14 0.33
23 7 0.16
24 22 0.51
ACGTcount: A:0.24, C:0.36, G:0.15, T:0.24
Consensus pattern (23 bp):
GTGTCACAACTCTAAACCCTGCC
Found at i:6432371 original size:81 final size:81
Alignment explanation
Indices: 6432279--6432456 Score: 284
Period size: 81 Copynumber: 2.2 Consensus size: 81
6432269 CACACGTCTG
* * *
6432279 ACCATGCCGTGTCACAAACTCTATACCCTGCCGTGTCACACCCGTCTCATATATTCTCACAATGA
1 ACCATGCCGTGTCACAAACTCTATACCCTGCCATATCACACCCGTCTCACATATTCTCACAATGA
*
6432344 CGTGTCACACATTGCC
66 CGTGTCACACATTCCC
* * * *
6432360 ACCATGTCGTGTCACAAACTCTATACCCTGCCATATGACACCCGTCTTACATATTCTCACATTGA
1 ACCATGCCGTGTCACAAACTCTATACCCTGCCATATCACACCCGTCTCACATATTCTCACAATGA
6432425 CGTGTCACACATTCCC
66 CGTGTCACACATTCCC
6432441 ACCATGCCGTGTCACA
1 ACCATGCCGTGTCACA
6432457 CATTCCCACC
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 88 1.00
ACGTcount: A:0.25, C:0.35, G:0.13, T:0.26
Consensus pattern (81 bp):
ACCATGCCGTGTCACAAACTCTATACCCTGCCATATCACACCCGTCTCACATATTCTCACAATGA
CGTGTCACACATTCCC
Found at i:6432451 original size:23 final size:23
Alignment explanation
Indices: 6432425--6432479 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
6432415 CTCACATTGA
6432425 CGTGTCACACATTCCCACCATGC
1 CGTGTCACACATTCCCACCATGC
6432448 CGTGTCACACATTCCCACCATGC
1 CGTGTCACACATTCCCACCATGC
*
6432471 CGTTTCACA
1 CGTGTCACA
6432480 AACTCTAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.22, C:0.42, G:0.13, T:0.24
Consensus pattern (23 bp):
CGTGTCACACATTCCCACCATGC
Found at i:6438691 original size:49 final size:49
Alignment explanation
Indices: 6438550--6438705 Score: 240
Period size: 49 Copynumber: 3.2 Consensus size: 49
6438540 AACTTTTAGT
**
6438550 AAAGTGTTCAGATTTTTTAAACAATTTCATATTTTCATTTCTGTTAGCA
1 AAAGTGTTCAGATAATTTAAACAATTTCATATTTTCATTTCTGTTAGCA
* * *
6438599 AAAGTGTTTAGATAATTTAGAACAAATTCATATTTTCATTTCTGCTAGCA
1 AAAGTGTTCAGATAATTTA-AACAATTTCATATTTTCATTTCTGTTAGCA
* *
6438649 AAAGTGTTCAGGTACTTTAAACAATTTCATATTTTCATTTCTGTTAGCA
1 AAAGTGTTCAGATAATTTAAACAATTTCATATTTTCATTTCTGTTAGCA
6438698 AAAGTGTT
1 AAAGTGTT
6438706 TAGGGTGGCA
Statistics
Matches: 96, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
49 52 0.54
50 44 0.46
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (49 bp):
AAAGTGTTCAGATAATTTAAACAATTTCATATTTTCATTTCTGTTAGCA
Found at i:6440118 original size:15 final size:15
Alignment explanation
Indices: 6440095--6440154 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 15
6440085 TAATTACTGA
*
6440095 AAATTTAAATTGATT
1 AAATCTAAATTGATT
*
6440110 AAATCTAAAATT-ACTGA
1 AAATCT-AAATTGA-T-T
*
6440127 AAATTTAAATTGATT
1 AAATCTAAATTGATT
6440142 AAATCTAACATTG
1 AAATCTAA-ATTG
6440155 GGTGTTTTGC
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
15 13 0.37
16 16 0.46
17 6 0.17
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (15 bp):
AAATCTAAATTGATT
Found at i:6440127 original size:32 final size:32
Alignment explanation
Indices: 6440086--6440149 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
6440076 TCATTCCTGT
6440086 AATTACTGAAAATTTAAATTGATTAAATCTAA
1 AATTACTGAAAATTTAAATTGATTAAATCTAA
6440118 AATTACTGAAAATTTAAATTGATTAAATCTAA
1 AATTACTGAAAATTTAAATTGATTAAATCTAA
6440150 CATTGGGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (32 bp):
AATTACTGAAAATTTAAATTGATTAAATCTAA
Found at i:6451705 original size:14 final size:15
Alignment explanation
Indices: 6451676--6451708 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
6451666 ATGCCAAAAG
*
6451676 AAAATAAAATAGATA
1 AAAATAAAATAAATA
6451691 AAAATAAAA-AAATA
1 AAAATAAAATAAATA
6451705 AAAA
1 AAAA
6451709 CCCGGAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (15 bp):
AAAATAAAATAAATA
Found at i:6456486 original size:12 final size:12
Alignment explanation
Indices: 6456471--6456558 Score: 71
Period size: 10 Copynumber: 7.4 Consensus size: 12
6456461 TAATCTAATC
*
6456471 TATAATCTATTA
1 TATAATATATTA
6456483 TATATATATATATA
1 TATA-ATATAT-TA
6456497 TATATATATATATA
1 TATA-ATATAT-TA
*
6456511 TATAATA-ANTA
1 TATAATATATTA
6456522 TAT-ATATA-TA
1 TATAATATATTA
6456532 TAT-ATATA-TA
1 TATAATATATTA
6456542 TAT-ATATATATA
1 TATAATATAT-TA
6456554 TATAA
1 TATAA
6456559 ATACATATGT
Statistics
Matches: 68, Mismatches: 2, Indels: 11
0.84 0.02 0.14
Matches are distributed among these distances:
10 23 0.34
11 6 0.09
12 10 0.15
13 9 0.13
14 20 0.29
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.48
Consensus pattern (12 bp):
TATAATATATTA
Found at i:6456488 original size:2 final size:2
Alignment explanation
Indices: 6456481--6456557 Score: 131
Period size: 2 Copynumber: 39.0 Consensus size: 2
6456471 TATAATCTAT
6456481 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA -A NTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
6456522 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6456558 AATACATATG
Statistics
Matches: 72, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.03
2 69 0.96
3 1 0.01
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6458822 original size:27 final size:27
Alignment explanation
Indices: 6458792--6458849 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
6458782 TATTATTTAT
* * * *
6458792 TTTATTTTAATTATTAATAATTTATCA
1 TTTATTTAAAATAGTAATAATTAATCA
*
6458819 TTTATTTAAAATAGTAATAATTAATTA
1 TTTATTTAAAATAGTAATAATTAATCA
6458846 TTTA
1 TTTA
6458850 AATATTTATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (27 bp):
TTTATTTAAAATAGTAATAATTAATCA
Found at i:6458997 original size:29 final size:27
Alignment explanation
Indices: 6458963--6459018 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
6458953 ATTTTTAAAT
6458963 TTAAAATATTAACAT-TTTATAGTATAATA
1 TTAAAAT-TTAA-ATATTT-TAGTATAATA
*
6458992 TTAAAATTTAAATATTTTATTATAATA
1 TTAAAATTTAAATATTTTAGTATAATA
6459019 AGATTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 11 0.44
28 7 0.28
29 7 0.28
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
TTAAAATTTAAATATTTTAGTATAATA
Found at i:6459146 original size:8 final size:8
Alignment explanation
Indices: 6459133--6459166 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
6459123 TTTATTTTTA
6459133 TTAAAATT
1 TTAAAATT
*
6459141 TTAAAAGT
1 TTAAAATT
6459149 TTAAAATT
1 TTAAAATT
6459157 TTAATAATT
1 TTAA-AATT
6459166 T
1 T
6459167 ATCATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 18 0.78
9 5 0.22
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (8 bp):
TTAAAATT
Found at i:6459335 original size:46 final size:45
Alignment explanation
Indices: 6459216--6459335 Score: 111
Period size: 43 Copynumber: 2.6 Consensus size: 45
6459206 ATTTTTGCTG
* * * **
6459216 AAAAT-TTAAAATATTAAAAATTTAATAAATTAACTATTAATATTGTT
1 AAAATATT-AAATATT-ATAATTTAA-AATTTAAATATTAATATCATT
* * *
6459263 AAAATATT-AATATT-TTATTTATAATTTAAATATTATTATCATT
1 AAAATATTAAATATTATAATTTAAAATTTAAATATTAATATCATT
6459306 AAAATATTAAATATTAGTAATTTAAAATTT
1 AAAATATTAAATATTA-TAATTTAAAATTT
6459336 TTAATAAAGA
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
43 24 0.41
44 11 0.19
46 17 0.29
47 5 0.08
48 2 0.03
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (45 bp):
AAAATATTAAATATTATAATTTAAAATTTAAATATTAATATCATT
Found at i:6459339 original size:24 final size:23
Alignment explanation
Indices: 6459287--6459341 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
6459277 TTATTTATAA
*
6459287 TTTAAATATTATTATCATTAAAAT
1 TTTAAATATTATAAT-ATTAAAAT
*
6459311 ATTAAATATTAGTAAT-TTAAAAT
1 TTTAAATATTA-TAATATTAAAAT
*
6459334 TTTTAATA
1 TTTAAATA
6459342 AAGAGCATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 13 0.50
24 10 0.38
25 3 0.12
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
TTTAAATATTATAATATTAAAAT
Found at i:6459502 original size:100 final size:100
Alignment explanation
Indices: 6459389--6459580 Score: 341
Period size: 100 Copynumber: 1.9 Consensus size: 100
6459379 CCTCAACCAA
*
6459389 AGAATAGCAAATCTCAAGGA-AGGGTTGGGATTAGTTAAGCCTTATTTTTGGAAGATTTTGGAGA
1 AGAATAGCAAATCTC-AGGAGAGGGTTGGGATTAGTTAAGCCTTATTTTTGGAAGATTTTGGAAA
*
6459453 TTAGTTATTATAAGAAGATAACTATTCCCCCATCAT
65 TTAGTTATTAGAAGAAGATAACTATTCCCCCATCAT
*
6459489 AGAATAGCAAATCTCAGGAGAGGGTTGGGATTAGTTAAGCCTTGTTTTTGGAAGATTTTGGAAAT
1 AGAATAGCAAATCTCAGGAGAGGGTTGGGATTAGTTAAGCCTTATTTTTGGAAGATTTTGGAAAT
6459554 TAGTTATTAGAAGAAGATAACTATTCC
66 TAGTTATTAGAAGAAGATAACTATTCC
6459581 TTGAACCATT
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
99 4 0.05
100 84 0.95
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (100 bp):
AGAATAGCAAATCTCAGGAGAGGGTTGGGATTAGTTAAGCCTTATTTTTGGAAGATTTTGGAAAT
TAGTTATTAGAAGAAGATAACTATTCCCCCATCAT
Found at i:6461546 original size:15 final size:14
Alignment explanation
Indices: 6461526--6461555 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
6461516 CTTTGGAATA
6461526 AAAAAAATAGAAAAT
1 AAAAAAATA-AAAAT
6461541 AAAAAAATAAAAAT
1 AAAAAAATAAAAAT
6461555 A
1 A
6461556 TATTTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (14 bp):
AAAAAAATAAAAAT
Found at i:6461645 original size:25 final size:25
Alignment explanation
Indices: 6461617--6461665 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
6461607 TATAATTAAT
6461617 TAAAATATTAATAATTAAACTATAC
1 TAAAATATTAATAATTAAACTATAC
* * *
6461642 TAAAATATTGATATTTAAATTATA
1 TAAAATATTAATAATTAAACTATA
6461666 AATTATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (25 bp):
TAAAATATTAATAATTAAACTATAC
Found at i:6471717 original size:5 final size:5
Alignment explanation
Indices: 6471707--6471738 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
6471697 AAGAGTCAGT
6471707 GGAAA GGAAA GGAAA GGAAA GGAAA GGGAAA G
1 GGAAA GGAAA GGAAA GGAAA GGAAA -GGAAA G
6471739 ATAAGTCAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (5 bp):
GGAAA
Found at i:6484784 original size:4 final size:4
Alignment explanation
Indices: 6484775--6484801 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
6484765 TGCAAAGCGA
6484775 AAGC AAGC AAGC AAGC AAGC AAGC AAG
1 AAGC AAGC AAGC AAGC AAGC AAGC AAG
6484802 AGGAAGGGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.26, T:0.00
Consensus pattern (4 bp):
AAGC
Found at i:6492838 original size:21 final size:19
Alignment explanation
Indices: 6492814--6492853 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
6492804 TTTTACATAA
6492814 TATTTAAATAAATTTTCAAAT
1 TATTTAAA-AAATTTT-AAAT
6492835 TATTTAAAAAATTTTAAAT
1 TATTTAAAAAATTTTAAAT
6492854 AAATCTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
21 8 0.42
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
TATTTAAAAAATTTTAAAT
Found at i:6493102 original size:33 final size:33
Alignment explanation
Indices: 6493065--6493141 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 33
6493055 TGTTATCATC
* *
6493065 AATTATGATATGTCAACATGTTATATCATTATT
1 AATTATAATATGTCAACATGCTATATCATTATT
6493098 AATTATAATATGTCAACATGCTATATCATTATT
1 AATTATAATATGTCAACATGCTATATCATTATT
6493131 AATTATAATAT
1 AATTATAATAT
6493142 ATGAATATAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.44
Consensus pattern (33 bp):
AATTATAATATGTCAACATGCTATATCATTATT
Found at i:6493251 original size:30 final size:30
Alignment explanation
Indices: 6493215--6493271 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
6493205 TATTAGTTAT
*
6493215 AAAGATTTATTTGACTCAAAAGAAAAATAC
1 AAAGATTTATTTAACTCAAAAGAAAAATAC
* *
6493245 AAAGATTTATTTAACTCTAAATAAAAA
1 AAAGATTTATTTAACTCAAAAGAAAAA
6493272 AATATAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.54, C:0.09, G:0.07, T:0.30
Consensus pattern (30 bp):
AAAGATTTATTTAACTCAAAAGAAAAATAC
Found at i:6500617 original size:2 final size:2
Alignment explanation
Indices: 6500610--6500654 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
6500600 CAAATACACT
6500610 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6500652 TA T
1 TA T
6500655 TTTCATTTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6502548 original size:2 final size:2
Alignment explanation
Indices: 6502541--6502600 Score: 70
Period size: 2 Copynumber: 30.0 Consensus size: 2
6502531 TGTACTTGTC
* *
6502541 AT AT AT AT AT -T AT AT AT AT AT AT AC AT AC AT AT ACT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT -AT AT
6502584 A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
6502601 TCATTTATTC
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
1 2 0.04
2 44 0.88
3 4 0.08
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:6511327 original size:13 final size:13
Alignment explanation
Indices: 6511293--6511325 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
6511283 CTTTTTCTAT
6511293 TTTAAAAATCAAA
1 TTTAAAAATCAAA
*
6511306 ATTAAAAAT-AAA
1 TTTAAAAATCAAA
6511318 TTTAAAAA
1 TTTAAAAA
6511326 ATCATAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (13 bp):
TTTAAAAATCAAA
Found at i:6525553 original size:14 final size:13
Alignment explanation
Indices: 6525534--6525588 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 13
6525524 TATTTGTATT
6525534 AATTATTAAATAAA
1 AATTATTAAA-AAA
6525548 AATTATTAAAAAA
1 AATTATTAAAAAA
*
6525561 ATTTATT--AAAA
1 AATTATTAAAAAA
6525572 AATT-TT-AAAAA
1 AATTATTAAAAAA
6525583 AATTAT
1 AATTAT
6525589 ATAATAGGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
10 2 0.05
11 15 0.41
12 1 0.03
13 9 0.24
14 10 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AATTATTAAAAAA
Found at i:6525559 original size:10 final size:11
Alignment explanation
Indices: 6525545--6525588 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 11
6525535 ATTATTAAAT
6525545 AAAAATTATTAA
1 AAAAATTATT-A
6525557 AAAAATTTATTA
1 AAAAA-TTATTA
6525569 AAAAATT-TTAA
1 AAAAATTATT-A
6525580 AAAAATTAT
1 AAAAATTAT
6525589 ATAATAGGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.07
11 10 0.34
12 12 0.41
13 5 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AAAAATTATTA
Found at i:6525566 original size:13 final size:13
Alignment explanation
Indices: 6525536--6525586 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
6525526 TTTGTATTAA
*
6525536 TTATTAAATAAAAA
1 TTATTAAA-AAAAT
6525550 TTATTAAAAAAAT
1 TTATTAAAAAAAT
6525563 TTATT-AAAAAA-
1 TTATTAAAAAAAT
6525574 TT-TTAAAAAAAT
1 TTATTAAAAAAAT
6525586 T
1 T
6525587 ATATAATAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
10 2 0.06
11 8 0.24
12 7 0.21
13 9 0.26
14 8 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATTAAAAAAAT
Found at i:6538934 original size:22 final size:22
Alignment explanation
Indices: 6538901--6538952 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
6538891 AATTTTACTT
6538901 TTATTAATTTTTATAATTATAA
1 TTATTAATTTTTATAATTATAA
* *
6538923 TTATATAA-TTTTATTATTAT-T
1 TTAT-TAATTTTTATAATTATAA
6538944 TTATTAATT
1 TTATTAATT
6538953 AAAAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 3 0.12
21 5 0.19
22 15 0.58
23 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTATTAATTTTTATAATTATAA
Found at i:6539115 original size:27 final size:28
Alignment explanation
Indices: 6539050--6539115 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 28
6539040 AATGCTCTTT
6539050 ATTTTTTT-TTAAAAAAATATAATAATA
1 ATTTTTTTATTAAAAAAATATAATAATA
** **
6539077 ATTTTTAAATTAATAAAAA-AT-ATTTTA
1 ATTTTTTTATTAA-AAAAATATAATAATA
6539104 ATTTTTTTATTA
1 ATTTTTTTATTA
6539116 TTTTTATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
27 20 0.65
28 6 0.19
29 5 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
ATTTTTTTATTAAAAAAATATAATAATA
Found at i:6539987 original size:29 final size:31
Alignment explanation
Indices: 6539954--6540021 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 31
6539944 TATTTTTATT
6539954 ATAATTTAATAATTTTT-TTAT-ATTAAAAA
1 ATAATTTAATAATTTTTATTATAATTAAAAA
* *
6539983 ATAA-TTAA-ATTTTTTATTATAATTAAACA
1 ATAATTTAATAATTTTTATTATAATTAAAAA
6540012 AT-ATTTAATA
1 ATAATTTAATA
6540022 TTAAAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
27 6 0.18
28 9 0.27
29 17 0.52
30 1 0.03
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (31 bp):
ATAATTTAATAATTTTTATTATAATTAAAAA
Found at i:6540816 original size:31 final size:31
Alignment explanation
Indices: 6540778--6541072 Score: 428
Period size: 31 Copynumber: 9.5 Consensus size: 31
6540768 GTGTCAGCGT
6540778 TGGCGTGTTACAACATTTTACGTTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
* *
6540809 TGGCGTGTTACAACATTTTAAGTTATATACA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
*
6540840 TGGCGTGTTACAACATTTTATGTTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
** * * *
6540871 TGAAGTGTTACCACATTATATGTTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
*
6540902 TGGCGTGTTACAACATTATACGTTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
6540933 TGGCGTGTTACAACATTTTACGTTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
*
6540964 TGGCGTGTTACAACATTTTATGTTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
** * *
6540995 TGAAGTGTTACCACATTTTATGTTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
* *
6541026 TGGCGTGTTACGATATTTTACGTTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
* *
6541057 TGGCATGTTATAACAT
1 TGGCGTGTTACAACAT
6541073 GATTGACAAA
Statistics
Matches: 238, Mismatches: 26, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 238 1.00
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.40
Consensus pattern (31 bp):
TGGCGTGTTACAACATTTTACGTTATATGCA
Found at i:6545058 original size:118 final size:118
Alignment explanation
Indices: 6544848--6545386 Score: 700
Period size: 118 Copynumber: 4.6 Consensus size: 118
6544838 TATGCTAAGC
* ** *
6544848 TGACACGTTGAGTGCATGCAGATTTCTGTGGTGACACATTGACTTCTTGCATTATTGTGGGGTGA
1 TGACACGCTGAGTGCATGCAGATTTCTGTGGTGACACGCTGACTTCTTGCAGTATTGTGGGGTGA
* * *
6544913 TACGGCACACCCCATCTTGTGGTGACACGCTGAGTGGAACCAGATAGTTGGCG
66 CACGGCACGCCCCATCTTGTGGTGACACGCTGAGTGGAAGCAGATAGTTGGCG
* * * * *
6544966 TAACACGCTAAGTGCATGCAGATTTCTGTGATGACATGCTGACTTCTTGCAGTATTGTGGAGTGA
1 TGACACGCTGAGTGCATGCAGATTTCTGTGGTGACACGCTGACTTCTTGCAGTATTGTGGGGTGA
* * * *
6545031 CACGGCACGCCCTATCTTGTGGTGACACGCTAAGTGGAAGCAGATAGTTGACA
66 CACGGCACGCCCCATCTTGTGGTGACACGCTGAGTGGAAGCAGATAGTTGGCG
* * * *
6545084 TGACATGCTGAGTGCATGCAGATTTCTGTGGTGAGACACTGACTTCTTGCATTATTGTGGGGTGA
1 TGACACGCTGAGTGCATGCAGATTTCTGTGGTGACACGCTGACTTCTTGCAGTATTGTGGGGTGA
* * * *
6545149 CACGACAAGCCCCATTTTGTGGTGACACGCTGAGTGGAAGTAGATAGTTGGCG
66 CACGGCACGCCCCATCTTGTGGTGACACGCTGAGTGGAAGCAGATAGTTGGCG
* * * * * * * * * * * * *
6545202 TGACATGGTGACTTCTTGCTGATTTCTATGATAACACGTTGATTTCTTGTAGTATTGTGGGATGA
1 TGACACGCTGAGTGCATGCAGATTTCTGTGGTGACACGCTGACTTCTTGCAGTATTGTGGGGTGA
* *
6545267 CACAGCACGCCCCATTTTGTGGTGACACGCTGAGTGGAAGCAGATAGTTGGCG
66 CACGGCACGCCCCATCTTGTGGTGACACGCTGAGTGGAAGCAGATAGTTGGCG
* * *
6545320 TGACACGCTGAGTGCATGCAGATTTTTATGGTGACACGCTGACTTCTTGCTGTATTGTGGGGTGA
1 TGACACGCTGAGTGCATGCAGATTTCTGTGGTGACACGCTGACTTCTTGCAGTATTGTGGGGTGA
6545385 CA
66 CA
6545387 TGATGAGTAG
Statistics
Matches: 355, Mismatches: 66, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
118 355 1.00
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (118 bp):
TGACACGCTGAGTGCATGCAGATTTCTGTGGTGACACGCTGACTTCTTGCAGTATTGTGGGGTGA
CACGGCACGCCCCATCTTGTGGTGACACGCTGAGTGGAAGCAGATAGTTGGCG
Found at i:6545354 original size:31 final size:30
Alignment explanation
Indices: 6545280--6545361 Score: 92
Period size: 31 Copynumber: 2.7 Consensus size: 30
6545270 AGCACGCCCC
* *
6545280 ATTTTGTGGTGACACGCTGAGTGGAAGCAG
1 ATTTTTTGGTGACACGCTGAGTGCAAGCAG
** * *
6545310 ATAGTTGGCGTGACACGCTGAGTGCATGCAG
1 ATTTTTTG-GTGACACGCTGAGTGCAAGCAG
6545341 ATTTTTATGGTGACACGCTGA
1 ATTTTT-TGGTGACACGCTGA
6545362 CTTCTTGCTG
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
30 4 0.10
31 36 0.88
32 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.33, T:0.28
Consensus pattern (30 bp):
ATTTTTTGGTGACACGCTGAGTGCAAGCAG
Found at i:6547681 original size:145 final size:143
Alignment explanation
Indices: 6547501--6547811 Score: 371
Period size: 145 Copynumber: 2.2 Consensus size: 143
6547491 TATGTAGAAA
* ** * *
6547501 TGTTGAACACAAACTGTTAGAACTGATCTTACCGACGGGTCGTTAGCACTGTGCGTCTGAGGAA-
1 TGTTGAACACAAACTGTTAGAACTCATCTTACCGACGCCTCGTTAGCACTGTGAGTCTGA-AAAG
* *
6547565 GACCTCTC-AGTGGTTAAGAAGCTGTCATCGCATGGTCCAACTGTAAACACAGATATATTATTCA
65 GACCTATCGA-TGGTTAAGAAGCTGTCATCGCATGGTCCAACTGCAAACAC--ATATATTATTCA
6547629 ATAATCACATATGGAAT
127 ATAATCACATATGGAAT
* *
6547646 TGTTGAACACAAA-TCGTTATAA-TCATCATTACCGACTCCTCGTTAGCACTGTGAGTCTGAAAA
1 TGTTGAACACAAACT-GTTAGAACTCATC-TTACCGACGCCTCGTTAGCACTGTGAGTCTGAAAA
** * * * * *
6547709 GGACCTATCGATGGTTGTGGAGTTGTCGTCGCATGGTCCAACTGCAAACACATATGTTATTCGAT
64 GGACCTATCGATGGTTAAGAAGCTGTCATCGCATGGTCCAACTGCAAACACATATATTATTCAAT
6547774 AATCACATATGGAAT
129 AATCACATATGGAAT
*
6547789 TATTGAACACAAACCT-TTAGAAC
1 TGTTGAACACAAA-CTGTTAGAAC
6547812 CGTTCTTACC
Statistics
Matches: 141, Mismatches: 18, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
143 44 0.31
144 7 0.05
145 89 0.63
146 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (143 bp):
TGTTGAACACAAACTGTTAGAACTCATCTTACCGACGCCTCGTTAGCACTGTGAGTCTGAAAAGG
ACCTATCGATGGTTAAGAAGCTGTCATCGCATGGTCCAACTGCAAACACATATATTATTCAATAA
TCACATATGGAAT
Found at i:6549224 original size:31 final size:31
Alignment explanation
Indices: 6549191--6549362 Score: 238
Period size: 31 Copynumber: 5.5 Consensus size: 31
6549181 GTTAACCTAT
*
6549191 AATGTGGTAACACGCCATGCATATAACGTAT
1 AATGTGGTAACACGCCATGCATATAACGTAA
* **
6549222 AATATGGTAACACATCATGCATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
*
6549253 AATGTGATAACACGCCATGCATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
*
6549284 AATGTGGTAACACGCCATACATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
* * *
6549315 AATGTCGTAACACGCCATGCGTATCAA-GTCA
1 AATGTGGTAACACGCCATGCATAT-AACGTAA
*
6549346 AATGTTGTAACACGCCA
1 AATGTGGTAACACGCCA
6549363 ACGCTGACAC
Statistics
Matches: 125, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
31 123 0.98
32 2 0.02
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (31 bp):
AATGTGGTAACACGCCATGCATATAACGTAA
Found at i:6550933 original size:20 final size:20
Alignment explanation
Indices: 6550896--6550934 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
6550886 TTAATATTTT
*
6550896 TTATAAAATAATTTTTTAAA
1 TTATAAAATAATTATTTAAA
6550916 TTATAAAA-AATATATTTAA
1 TTATAAAATAAT-TATTTAA
6550935 TCTAATCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTATAAAATAATTATTTAAA
Found at i:6555626 original size:31 final size:31
Alignment explanation
Indices: 6555591--6555655 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 31
6555581 AGATGAAATG
6555591 TTAAA-AAAATAACAATAAAATTATAAAATTT
1 TTAAACAAAATAACAATAAAATTAT-AAATTT
**
6555622 TTAAACAAAATAATGATAAAATTATAAATTT
1 TTAAACAAAATAACAATAAAATTATAAATTT
6555653 TTA
1 TTA
6555656 GAAGTTTGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 14 0.45
32 17 0.55
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (31 bp):
TTAAACAAAATAACAATAAAATTATAAATTT
Found at i:6569683 original size:27 final size:27
Alignment explanation
Indices: 6569645--6569702 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
6569635 CATCTCCCAG
*
6569645 ATTCTGCTATGGCTCCCTTGGAAAACA
1 ATTCTGCTATGGCTCCCCTGGAAAACA
6569672 ATTCTGCTATGGCTCCCCTGGAAAACA
1 ATTCTGCTATGGCTCCCCTGGAAAACA
6569699 ATTC
1 ATTC
6569703 ATCCAATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (27 bp):
ATTCTGCTATGGCTCCCCTGGAAAACA
Found at i:6589324 original size:22 final size:22
Alignment explanation
Indices: 6589298--6589366 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
6589288 TAAAATATCA
* *
6589298 TATTAGTATTTTAATAA-ACAGT
1 TATTAATATTTTAATAATA-AAT
*
6589320 TATTAATATTTTAGTAATAAAT
1 TATTAATATTTTAATAATAAAT
* *
6589342 TATTAATATTTTAATCATATAT
1 TATTAATATTTTAATAATAAAT
6589364 TAT
1 TAT
6589367 GAAAAAAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
22 39 0.98
23 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (22 bp):
TATTAATATTTTAATAATAAAT
Found at i:6589395 original size:22 final size:21
Alignment explanation
Indices: 6589370--6589425 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
6589360 ATATTATGAA
*
6589370 AAAAATTAAAAGAGAAAAAGGT
1 AAAAATTAAAAGAGAAAAA-AT
*
6589392 AAAAATGAAAATAGAGAAAAAAT
1 AAAAAT-TAAA-AGAGAAAAAAT
*
6589415 AAAAACTAAAA
1 AAAAATTAAAA
6589426 ATCATATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
21 1 0.04
22 9 0.32
23 9 0.32
24 9 0.32
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.12
Consensus pattern (21 bp):
AAAAATTAAAAGAGAAAAAAT
Found at i:6589426 original size:24 final size:24
Alignment explanation
Indices: 6589380--6589427 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
6589370 AAAAATTAAA
* *
6589380 AGAGAAAAAGGTAAAAATGAAAAT
1 AGAGAAAAAGATAAAAATAAAAAT
6589404 AGAGAAAAA-ATAAAAACTAAAAAT
1 AGAGAAAAAGATAAAAA-TAAAAAT
6589428 CATATTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.71, C:0.02, G:0.15, T:0.12
Consensus pattern (24 bp):
AGAGAAAAAGATAAAAATAAAAAT
Found at i:6592531 original size:69 final size:69
Alignment explanation
Indices: 6592390--6592542 Score: 166
Period size: 69 Copynumber: 2.2 Consensus size: 69
6592380 AGTGTGGGGA
* * * *
6592390 TAAGAATACCACATGGTTAAGTTGGACATCGTACCACTTTTCCCCTCCTCATGAGTCTCGATGTG
1 TAAGAATACCACAAGATTAAGTTGGACATCGTACCACTTCTCCCCTCCTCATGAGTCTCGATGTA
* *
6592455 GGGG
66 AGAG
*** *
6592459 TAAGAATACCACAAGATTAAGTTAGG-CATCGTACCACTTCTCTTTTCCTTATGAGTCTC-AGTG
1 TAAGAATACCACAAGATTAAGTT-GGACATCGTACCACTTCTCCCCTCCTCATGAGTCTCGA-TG
*
6592522 TAATAG
64 TAAGAG
*
6592528 TAAGAATATCACAAG
1 TAAGAATACCACAAG
6592543 GACGAGTTAG
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
68 1 0.01
69 67 0.96
70 2 0.03
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (69 bp):
TAAGAATACCACAAGATTAAGTTGGACATCGTACCACTTCTCCCCTCCTCATGAGTCTCGATGTA
AGAG
Found at i:6608334 original size:13 final size:13
Alignment explanation
Indices: 6608316--6608341 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6608306 TTAATTTATC
6608316 AAAAATTTTAATT
1 AAAAATTTTAATT
6608329 AAAAATTTTAATT
1 AAAAATTTTAATT
6608342 GGTCATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAAATTTTAATT
Found at i:6629794 original size:30 final size:31
Alignment explanation
Indices: 6629734--6629794 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
6629724 GAATAAAGGG
*
6629734 AGAAGGAAGAAGGAAGCAGAAAGAAGAGAAT
1 AGAAGGAAGAAGGAAGCAGAAAGAAAAGAAT
* *
6629765 AGAAGG-AGAAGGAAGCAGAGATAAAAGAAT
1 AGAAGGAAGAAGGAAGCAGAAAGAAAAGAAT
6629795 GGGTGAGAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.57, C:0.03, G:0.34, T:0.05
Consensus pattern (31 bp):
AGAAGGAAGAAGGAAGCAGAAAGAAAAGAAT
Found at i:6639240 original size:29 final size:29
Alignment explanation
Indices: 6639207--6639303 Score: 115
Period size: 29 Copynumber: 3.3 Consensus size: 29
6639197 GAAAAAGTAT
* *
6639207 AAGAGAAGAAGTTGAATGAAAATATGTAC
1 AAGAGAAGAAGTTGTATGAAAATAGGTAC
**
6639236 AAGAGAAGAAGTTGTGCGAGAAA-AGGTAC
1 AAGAGAAGAAGTTGTATGA-AAATAGGTAC
* *
6639265 AAGAGAAGAAGCTGTATGAGAATAGGTAC
1 AAGAGAAGAAGTTGTATGAAAATAGGTAC
*
6639294 AGGAGAAGAA
1 AAGAGAAGAA
6639304 ACTGTACATG
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
28 2 0.04
29 52 0.91
30 3 0.05
ACGTcount: A:0.48, C:0.05, G:0.31, T:0.15
Consensus pattern (29 bp):
AAGAGAAGAAGTTGTATGAAAATAGGTAC
Found at i:6639308 original size:29 final size:29
Alignment explanation
Indices: 6639196--6639309 Score: 95
Period size: 29 Copynumber: 3.9 Consensus size: 29
6639186 GAGGCGTACA
* * ** *
6639196 AGAAAAAGTATAAGAGAAGAAGTTGAATG
1 AGAAAAGGTACAAGAGAAGAAACTGTATG
* ** **
6639225 A-AAATATGTACAAGAGAAGAAGTTGTGCG
1 AGAAA-AGGTACAAGAGAAGAAACTGTATG
*
6639254 AGAAAAGGTACAAGAGAAGAAGCTGTATG
1 AGAAAAGGTACAAGAGAAGAAACTGTATG
* *
6639283 AGAATAGGTACAGGAGAAGAAACTGTA
1 AGAAAAGGTACAAGAGAAGAAACTGTA
6639310 CATGAATTGG
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
28 3 0.04
29 65 0.92
30 3 0.04
ACGTcount: A:0.49, C:0.05, G:0.29, T:0.17
Consensus pattern (29 bp):
AGAAAAGGTACAAGAGAAGAAACTGTATG
Found at i:6639980 original size:41 final size:41
Alignment explanation
Indices: 6639935--6640066 Score: 160
Period size: 41 Copynumber: 3.2 Consensus size: 41
6639925 TTGTAATGTC
*
6639935 AATATCTTTTGTAATATTTGATTGATTATGCAATAATATTT
1 AATATCTTTTGTAATATTTGATTGATTATGTAATAATATTT
* * * ** *
6639976 AATATCTTTCGTAATATTTGACTGCATT-TTTTTTAATA-TC
1 AATATCTTTTGTAATATTTGATTG-ATTATGTAATAATATTT
* *
6640016 AATATCTTTTGTAATATTTTATTAATTATGTAATAATATTT
1 AATATCTTTTGTAATATTTGATTGATTATGTAATAATATTT
6640057 AATATCTTTT
1 AATATCTTTT
6640067 TCATAAAAAA
Statistics
Matches: 73, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
39 3 0.04
40 28 0.38
41 39 0.53
42 3 0.04
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.54
Consensus pattern (41 bp):
AATATCTTTTGTAATATTTGATTGATTATGTAATAATATTT
Found at i:6640031 original size:40 final size:39
Alignment explanation
Indices: 6639920--6640034 Score: 122
Period size: 41 Copynumber: 2.8 Consensus size: 39
6639910 CAAAATATAT
* *
6639920 TTTTTTTGTAATGTCAATATCTTTTGTAATATTTGATTGA
1 TTTTTTT-TAATATCAATATCTTTTGTAATATTTGACTGA
**** * *
6639960 TTATGCAATAATATTTAATATCTTTCGTAATATTTGACTGCA
1 TT-TTTTTTAATA-TCAATATCTTTTGTAATATTTGACTG-A
6640002 TTTTTTTTAATATCAATATCTTTTGTAATATTT
1 TTTTTTTTAATATCAATATCTTTTGTAATATTT
6640035 TATTAATTAT
Statistics
Matches: 58, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
40 25 0.43
41 30 0.52
42 3 0.05
ACGTcount: A:0.29, C:0.08, G:0.09, T:0.55
Consensus pattern (39 bp):
TTTTTTTTAATATCAATATCTTTTGTAATATTTGACTGA
Found at i:6640099 original size:66 final size:67
Alignment explanation
Indices: 6640023--6640156 Score: 234
Period size: 66 Copynumber: 2.0 Consensus size: 67
6640013 ATCAATATCT
6640023 TTTGTAATATTTTATTAATTATGTAATAATATTTAATATCTTTTTCAT-AAAAAAACCTTGATTC
1 TTTGTAATATTTTATTAATTATGTAATAATATTTAATATCTTTTTCATAAAAAAAACCTTGATTC
6640087 TA
66 TA
* * *
6640089 TTTGTTATATTTTATTGATTATGTAATAATATTTAATATCTTTTTCATAAAAAAAATCTTGATTC
1 TTTGTAATATTTTATTAATTATGTAATAATATTTAATATCTTTTTCATAAAAAAAACCTTGATTC
6640154 TA
66 TA
6640156 T
1 T
6640157 GTGACTTANG
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
66 46 0.72
67 18 0.28
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (67 bp):
TTTGTAATATTTTATTAATTATGTAATAATATTTAATATCTTTTTCATAAAAAAAACCTTGATTC
TA
Found at i:6640725 original size:25 final size:24
Alignment explanation
Indices: 6640675--6640726 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
6640665 CTTAGAAAAG
* * *
6640675 TGAATAAAAGAAGTAAATAAATGC
1 TGAATAAAAGAAGCAAACAAAGGC
*
6640699 TGAAGTAAAAGGAGCAAACAAAGGC
1 TGAA-TAAAAGAAGCAAACAAAGGC
6640724 TGA
1 TGA
6640727 CTAACTTGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.54, C:0.08, G:0.23, T:0.15
Consensus pattern (24 bp):
TGAATAAAAGAAGCAAACAAAGGC
Found at i:6643560 original size:26 final size:27
Alignment explanation
Indices: 6643513--6643567 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
6643503 GCCAAAAGGG
*
6643513 AACTCTCAACTTTACATCAAGGAGATT
1 AACTCTCAACTTGACATCAAGGAGATT
* * *
6643540 AACTCT-AACTTGATATGAAGGAGTTT
1 AACTCTCAACTTGACATCAAGGAGATT
6643566 AA
1 AA
6643568 TTCAACCCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (27 bp):
AACTCTCAACTTGACATCAAGGAGATT
Found at i:6643840 original size:103 final size:102
Alignment explanation
Indices: 6643635--6643908 Score: 307
Period size: 103 Copynumber: 2.7 Consensus size: 102
6643625 AGGGCCAAGA
* * * * * *
6643635 AATAAGCGATAAAACTTGTGGCCAATAGCATAACATCATTATAGCTAAATTATGAGCGATAAAGC
1 AATAAGCGATAAAGCTTGTGACCAATAGAAAAACATCATTATAGCCAAAATATGAGCGATAAAGC
* * * *
6643700 TAGCGGTTGAAATATGAATAATCAATTATGGTCAAAG
66 TAGCAGTTGAAATAAGAATAATCAACTATGGTAAAAG
* * * * *
6643737 AATAAGCGATAAAGCTTGCGATCAATAGAAAAATATCATTGTAGCCAAAATATGAGCGGTAAAAG
1 AATAAGCGATAAAGCTTGTGACCAATAGAAAAACATCATTATAGCCAAAATATGAGCGAT-AAAG
* *
6643802 CTTA-CAGTTGAAGTAAGAATAATGAACTATGGTAAAAG
65 C-TAGCAGTTGAAATAAGAATAATCAACTATGGTAAAAG
* * * * * * *
6643840 AATAAGCGATAAAGCTTGTGACCAATAGTATAATATAATTACAGCTAAAATATAAGCGATAAAGC
1 AATAAGCGATAAAGCTTGTGACCAATAGAAAAACATCATTATAGCCAAAATATGAGCGATAAAGC
6643905 TAGC
66 TAGC
6643909 GGCTGAATAT
Statistics
Matches: 142, Mismatches: 27, Indels: 6
0.81 0.15 0.03
Matches are distributed among these distances:
101 2 0.01
102 55 0.39
103 83 0.58
104 2 0.01
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.25
Consensus pattern (102 bp):
AATAAGCGATAAAGCTTGTGACCAATAGAAAAACATCATTATAGCCAAAATATGAGCGATAAAGC
TAGCAGTTGAAATAAGAATAATCAACTATGGTAAAAG
Found at i:6644901 original size:17 final size:16
Alignment explanation
Indices: 6644881--6644990 Score: 64
Period size: 14 Copynumber: 7.4 Consensus size: 16
6644871 TACAAGAAAA
6644881 TGTACAAGAGAAGAAG
1 TGTACAAGAGAAGAAG
*
6644897 TTGTAC--GAGAA-TA-
1 -TGTACAAGAGAAGAAG
6644910 TGTACAAGAGAAGAAG
1 TGTACAAGAGAAGAAG
* *
6644926 CTGTGC--GATAAG-AG
1 -TGTACAAGAGAAGAAG
6644940 -GTACAAGAGAAGAAG
1 TGTACAAGAGAAGAAG
*
6644955 CTGTAC-A-AGAA-TAG
1 -TGTACAAGAGAAGAAG
6644969 -GTACAAGAGAAGAAG
1 TGTACAAGAGAAGAAG
6644984 CTGTACA
1 -TGTACA
6644991 TGAATAGGTA
Statistics
Matches: 70, Mismatches: 8, Indels: 30
0.65 0.07 0.28
Matches are distributed among these distances:
12 12 0.17
13 1 0.01
14 19 0.27
15 19 0.27
16 1 0.01
17 18 0.26
ACGTcount: A:0.45, C:0.10, G:0.29, T:0.16
Consensus pattern (16 bp):
TGTACAAGAGAAGAAG
Found at i:6644902 original size:29 final size:29
Alignment explanation
Indices: 6644869--6645008 Score: 181
Period size: 29 Copynumber: 4.8 Consensus size: 29
6644859 AGAAAAGAGG
* * *
6644869 TGTACAAGAAAATGTACAAGAGAAGAAGT
1 TGTACAAGAATAGGTACAAGAGAAGAAGC
* *
6644898 TGTACGAGAATATGTACAAGAGAAGAAGC
1 TGTACAAGAATAGGTACAAGAGAAGAAGC
* * * *
6644927 TGTGCGATAAGAGGTACAAGAGAAGAAGC
1 TGTACAAGAATAGGTACAAGAGAAGAAGC
6644956 TGTACAAGAATAGGTACAAGAGAAGAAGC
1 TGTACAAGAATAGGTACAAGAGAAGAAGC
* *
6644985 TGTACATGAATAGGTACACGAGAA
1 TGTACAAGAATAGGTACAAGAGAA
6645009 CAAGGTAAGA
Statistics
Matches: 98, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 98 1.00
ACGTcount: A:0.46, C:0.10, G:0.28, T:0.16
Consensus pattern (29 bp):
TGTACAAGAATAGGTACAAGAGAAGAAGC
Found at i:6645313 original size:35 final size:35
Alignment explanation
Indices: 6645238--6645322 Score: 89
Period size: 35 Copynumber: 2.4 Consensus size: 35
6645228 ATGGATTAAT
* * * * * * *
6645238 GCTTTACTTATTTTAATTGTTTTGCTTTAAGGAGT
1 GCTTCACTTATTCTAATTGTTCTGCGTAAAGCAGC
*
6645273 ACTTCACTTATTCTAATTGTTCTGCGTAAAGCAGC
1 GCTTCACTTATTCTAATTGTTCTGCGTAAAGCAGC
*
6645308 GCTTCACTTGTTCTA
1 GCTTCACTTATTCTA
6645323 GTTATTTTGC
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.21, C:0.18, G:0.15, T:0.46
Consensus pattern (35 bp):
GCTTCACTTATTCTAATTGTTCTGCGTAAAGCAGC
Found at i:6645334 original size:35 final size:35
Alignment explanation
Indices: 6645273--6645365 Score: 96
Period size: 35 Copynumber: 2.7 Consensus size: 35
6645263 TTTAAGGAGT
* * *
6645273 ACTTCACTTATTCTAATTGTTCTGCGTAAAGCAGC
1 ACTTCACTTGTTCTAGTTATTCTGCGTAAAGCAGC
* * * *
6645308 GCTTCACTTGTTCTAGTTATTTTGCGTGAAGTAGC
1 ACTTCACTTGTTCTAGTTATTCTGCGTAAAGCAGC
* * *
6645343 ACTTTACTTGTTTTAGTTGTTCT
1 ACTTCACTTGTTCTAGTTATTCT
6645366 CTGTACAACA
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.19, C:0.18, G:0.17, T:0.45
Consensus pattern (35 bp):
ACTTCACTTGTTCTAGTTATTCTGCGTAAAGCAGC
Found at i:6649641 original size:15 final size:15
Alignment explanation
Indices: 6649608--6649650 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
6649598 AGTCTAAATT
6649608 TATAACTTAGAAA-ATA
1 TATAA-TTA-AAATATA
6649624 TATAATTAAAATATA
1 TATAATTAAAATATA
*
6649639 TATAATTTAAAT
1 TATAATTAAAAT
6649651 TACAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 3 0.12
15 17 0.68
16 5 0.20
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (15 bp):
TATAATTAAAATATA
Found at i:6651542 original size:73 final size:73
Alignment explanation
Indices: 6651423--6651569 Score: 267
Period size: 73 Copynumber: 2.0 Consensus size: 73
6651413 TTTCGGCACC
*
6651423 CTGTAAGCTCACATTCTGTTTTAATAAGTTCATATTGACTGTTCTGTTGGACTGATATATGGTGA
1 CTGTAAGCTCACATTCTGTTTTAATAAGCTCATATTGACTGTTCTGTTGGACTGATATATGGTGA
6651488 GCGAATCA
66 GCGAATCA
* *
6651496 CTGTAAGCTCACATTCTGTTTTAATAAGCTCATATTGACTGTTCTGTTGGACTTATCTATGGTGA
1 CTGTAAGCTCACATTCTGTTTTAATAAGCTCATATTGACTGTTCTGTTGGACTGATATATGGTGA
6651561 GCGAATCA
66 GCGAATCA
6651569 C
1 C
6651570 ATTTTTACCC
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (73 bp):
CTGTAAGCTCACATTCTGTTTTAATAAGCTCATATTGACTGTTCTGTTGGACTGATATATGGTGA
GCGAATCA
Found at i:6652075 original size:4 final size:4
Alignment explanation
Indices: 6652066--6652186 Score: 102
Period size: 4 Copynumber: 30.2 Consensus size: 4
6652056 CTTTTTTACT
* * * *
6652066 TATA TATA TATA TATA TATA TATA TATG TATG TATG TATG TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * *
6652114 TATG TATG TATG TAT- TGNTA CT-TA TATA TATA TATA TATA TATA TATA
1 TATA TATA TATA TATA T-ATA -TATA TATA TATA TATA TATA TATA TATA
* * * *
6652162 TGTA TGTA TGTA TGTA TATA TATA T
1 TATA TATA TATA TATA TATA TATA T
6652187 GTATGTATGT
Statistics
Matches: 107, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
3 2 0.02
4 104 0.97
6 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.10, T:0.50
Consensus pattern (4 bp):
TATA
Found at i:6652114 original size:24 final size:24
Alignment explanation
Indices: 6652082--6652198 Score: 154
Period size: 24 Copynumber: 5.0 Consensus size: 24
6652072 TATATATATA
6652082 TATATATATATGTATGTATGTATG
1 TATATATATATGTATGTATGTATG
6652106 TATATATATATGTATGTATGTATTG
1 TATATATATATGTATGTATGTA-TG
* *
6652131 NTACT-TATATA--TA--TATATATA
1 -TA-TATATATATGTATGTATGTATG
6652152 TATATATATATGTATGTATGTATG
1 TATATATATATGTATGTATGTATG
6652176 TATATATATATGTATGTATGTAT
1 TATATATATATGTATGTATGTAT
6652199 TGCATTCTAT
Statistics
Matches: 81, Mismatches: 4, Indels: 16
0.80 0.04 0.16
Matches are distributed among these distances:
19 1 0.01
20 8 0.10
21 1 0.01
22 7 0.09
24 53 0.65
25 2 0.02
26 8 0.10
27 1 0.01
ACGTcount: A:0.35, C:0.01, G:0.13, T:0.50
Consensus pattern (24 bp):
TATATATATATGTATGTATGTATG
Found at i:6652175 original size:70 final size:69
Alignment explanation
Indices: 6652062--6652200 Score: 269
Period size: 70 Copynumber: 2.0 Consensus size: 69
6652052 ATTTCTTTTT
6652062 TACTTATATATATATATATATATATATATATGTATGTATGTATGTATATATATATGTATGTATGT
1 TACTTATATATATATATATATATATATATATGTATGTATGTATGTATATATATATGTATGTATGT
6652127 ATTG
66 ATTG
6652131 NTACTTATATATATATATATATATATATATATGTATGTATGTATGTATATATATATGTATGTATG
1 -TACTTATATATATATATATATATATATATATGTATGTATGTATGTATATATATATGTATGTATG
6652196 TATTG
65 TATTG
6652201 CATTCTATTC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.36, C:0.01, G:0.12, T:0.50
Consensus pattern (69 bp):
TACTTATATATATATATATATATATATATATGTATGTATGTATGTATATATATATGTATGTATGT
ATTG
Found at i:6652187 original size:12 final size:12
Alignment explanation
Indices: 6652070--6652190 Score: 117
Period size: 12 Copynumber: 10.2 Consensus size: 12
6652060 TTTACTTATA
*
6652070 TATATATATATA
1 TATATATATATG
6652082 TATATATATATG
1 TATATATATATG
* *
6652094 TATGTATGTATG
1 TATATATATATG
6652106 TATATATATATG
1 TATATATATATG
* *
6652118 TATGTATGTATTG
1 TATATATATA-TG
6652131 NTACT-TATATA--
1 -TA-TATATATATG
6652142 TATATATATA--
1 TATATATATATG
6652152 TATATATATATG
1 TATATATATATG
* *
6652164 TATGTATGTATG
1 TATATATATATG
6652176 TATATATATATG
1 TATATATATATG
6652188 TAT
1 TAT
6652191 GTATGTATTG
Statistics
Matches: 91, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
9 1 0.01
10 18 0.20
12 62 0.68
13 2 0.02
14 7 0.08
15 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.11, T:0.50
Consensus pattern (12 bp):
TATATATATATG
Found at i:6652191 original size:4 final size:4
Alignment explanation
Indices: 6652090--6652198 Score: 94
Period size: 4 Copynumber: 26.8 Consensus size: 4
6652080 TATATATATA
* * *
6652090 TATG TATG TATG TATG TATA TATA TATG TATG TATG TATTG NTACT- TATA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA-TG -TA-TG TATG
* * * * * * *
6652140 TATA TATA TATA TATA TATA TATG TATG TATG TATG TATA TATA TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
6652188 TATG TATG TAT
1 TATG TATG TAT
6652199 TGCATTCTAT
Statistics
Matches: 96, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
3 1 0.01
4 90 0.94
5 2 0.02
6 3 0.03
ACGTcount: A:0.34, C:0.01, G:0.14, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:6655804 original size:14 final size:14
Alignment explanation
Indices: 6655785--6655811 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6655775 ATTATGTGTG
6655785 AATTTTCCTTTTTT
1 AATTTTCCTTTTTT
6655799 AATTTTCCTTTTT
1 AATTTTCCTTTTT
6655812 CTTTCTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (14 bp):
AATTTTCCTTTTTT
Found at i:6658242 original size:95 final size:94
Alignment explanation
Indices: 6658124--6658303 Score: 342
Period size: 95 Copynumber: 1.9 Consensus size: 94
6658114 ACAGAATGAG
*
6658124 TCATCACTAATGTGACATAAGTAATTATATTGTTTCTACAGGTAATCTGATCTGACAAAGTTAAT
1 TCATCACTAATGTGACATAAGTAATTATATTCTTTCTACAGGTAATCTGATCTGACAAAGTTAAT
6658189 TGACTTTAAGACAATACAATCTGATTGAT
66 TGACTTTAAGACAATACAATCTGATTGAT
6658218 TCATCACTAAATGTGACATAAGTAATTATATTCTTTCTACAGGTAATCTGATCTGACAAAGTTAA
1 TCATCACT-AATGTGACATAAGTAATTATATTCTTTCTACAGGTAATCTGATCTGACAAAGTTAA
6658283 TTGACTTTAAGACAATACAAT
65 TTGACTTTAAGACAATACAAT
6658304 ACTATTTCTT
Statistics
Matches: 84, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
94 8 0.10
95 76 0.90
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (94 bp):
TCATCACTAATGTGACATAAGTAATTATATTCTTTCTACAGGTAATCTGATCTGACAAAGTTAAT
TGACTTTAAGACAATACAATCTGATTGAT
Found at i:6664605 original size:2 final size:2
Alignment explanation
Indices: 6664594--6664644 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
6664584 AAGAAAATTA
6664594 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6664635 AT AT AT AT AT
1 AT AT AT AT AT
6664645 CCTGTATGAC
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:6683210 original size:14 final size:14
Alignment explanation
Indices: 6683193--6683220 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6683183 TATTTATATA
6683193 TAAAATAAATTATT
1 TAAAATAAATTATT
6683207 TAAAATAAATTATT
1 TAAAATAAATTATT
6683221 GATATATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAAAATAAATTATT
Found at i:6683876 original size:12 final size:13
Alignment explanation
Indices: 6683859--6683892 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
6683849 TTTAGGTTTG
*
6683859 CTTTTCTTTCTTT
1 CTTTTCTTTCCTT
6683872 C-TTTCTTTCCTT
1 CTTTTCTTTCCTT
6683884 CTTTTCTTT
1 CTTTTCTTT
6683893 GGTCTTTCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
CTTTTCTTTCCTT
Found at i:6683910 original size:22 final size:20
Alignment explanation
Indices: 6683875--6683914 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
6683865 TTTCTTTCTT
6683875 TCTTTCCTTCTTTTCTTTGG
1 TCTTTCCTTCTTTTCTTTGG
6683895 TCTTTCTCTTTCTTTTCTTT
1 TCTTTC-C-TTCTTTTCTTT
6683915 CTCTCTCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 1 0.06
22 11 0.61
ACGTcount: A:0.00, C:0.25, G:0.05, T:0.70
Consensus pattern (20 bp):
TCTTTCCTTCTTTTCTTTGG
Found at i:6687387 original size:62 final size:62
Alignment explanation
Indices: 6687312--6687437 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 62
6687302 GAATGTGATG
*
6687312 GGGTTGAGAAGCCAATAGCTTGCCAGAATGTTGCTTCTGTTGCACATAAATCCTTTGTTGTA
1 GGGTTGAGAAGCCAATAGCTTGCCAGAATGTTGCTTCTCTTGCACATAAATCCTTTGTTGTA
6687374 GGGTTGAGAAGCCAATAGCTTGCCAGAATGTTGCTTCTCTTGCACATAAATCCTTTGTTGTA
1 GGGTTGAGAAGCCAATAGCTTGCCAGAATGTTGCTTCTCTTGCACATAAATCCTTTGTTGTA
6687436 GG
1 GG
6687438 TTCGTATCAA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (62 bp):
GGGTTGAGAAGCCAATAGCTTGCCAGAATGTTGCTTCTCTTGCACATAAATCCTTTGTTGTA
Found at i:6694483 original size:2 final size:2
Alignment explanation
Indices: 6694476--6694503 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6694466 TAAATAATAA
6694476 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6694504 GCATACACTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6697786 original size:259 final size:259
Alignment explanation
Indices: 6697320--6697836 Score: 890
Period size: 259 Copynumber: 2.0 Consensus size: 259
6697310 GGAGAGTCAA
* *
6697320 AGGGTTCTTTGACAACCTTTTAGTGTACAGTCTATCAGTGTAATTCATTCCCTCATCATATATCC
1 AGGGTTATTTGACAACCTTTCAGTGTACAGTCTATCAGTGTAATTCATTCCCTCATCATATATCC
*
6697385 CGGAGATGATAAGAGTTTGGTACAGTGTCTACTCTTATTGACCTCCATATTTGTTCATGCAATTA
66 CGGAGATGATAAGAGCTTGGTACAGTGTCTACTCTTATTGACCTCCATATTTGTTCATGCAATTA
* *
6697450 TAACATTAGCTTTATAGAGAGTTATGAAACATTTTTCATAATCTCCATGTCGCATTGGCCAAGGA
131 TAACATTAGCTTTATAGAAAGTTATGAAACATTTTTCATAATCTCCATGTCACATTGGCCAAGGA
*
6697515 CTTCAATAAGCTAATGTTAACCAAAAACTAATAGGATATGTCATCTAAAACACTTGAGGTGATT
196 CTTCAATAAGCTAATGTTAACCAAAAACTAATAAGATATGTCATCTAAAACACTTGAGGTGATT
* *
6697579 AGGGTTATTTGACAACCTTTCAGTGTACAGTCTATCAGTGTAATTCATTCCTTCATCATATATCT
1 AGGGTTATTTGACAACCTTTCAGTGTACAGTCTATCAGTGTAATTCATTCCCTCATCATATATCC
* *
6697644 CGGAGATTATAAGAGCTTGGTACAGTGTCTACTCTTATTGACCTCCATATTTGTTCCTGCAATTA
66 CGGAGATGATAAGAGCTTGGTACAGTGTCTACTCTTATTGACCTCCATATTTGTTCATGCAATTA
* * * *
6697709 TAGCATTAGCTTTATAGAAAGTTATGAAACCTTTTTCATAATCTCCATGTTACCTTGGCCAAGGA
131 TAACATTAGCTTTATAGAAAGTTATGAAACATTTTTCATAATCTCCATGTCACATTGGCCAAGGA
* *
6697774 CTTCAATAAGCTAATGTTAACCAAGAACTAATAAGATATGTCCTCTAAAACACTTGAGGTGAT
196 CTTCAATAAGCTAATGTTAACCAAAAACTAATAAGATATGTCATCTAAAACACTTGAGGTGAT
6697837 AATTCCTATC
Statistics
Matches: 242, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
259 242 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.35
Consensus pattern (259 bp):
AGGGTTATTTGACAACCTTTCAGTGTACAGTCTATCAGTGTAATTCATTCCCTCATCATATATCC
CGGAGATGATAAGAGCTTGGTACAGTGTCTACTCTTATTGACCTCCATATTTGTTCATGCAATTA
TAACATTAGCTTTATAGAAAGTTATGAAACATTTTTCATAATCTCCATGTCACATTGGCCAAGGA
CTTCAATAAGCTAATGTTAACCAAAAACTAATAAGATATGTCATCTAAAACACTTGAGGTGATT
Found at i:6698654 original size:15 final size:17
Alignment explanation
Indices: 6698631--6698669 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 17
6698621 AAAATCATAT
6698631 TATA-TAAAAAT-T-AA
1 TATATTAAAAATATAAA
6698645 TA-ATTAAAAATATAAA
1 TATATTAAAAATATAAA
6698661 TATATTAAA
1 TATATTAAA
6698670 CTTATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.05
14 9 0.43
15 1 0.05
16 4 0.19
17 6 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TATATTAAAAATATAAA
Found at i:6698852 original size:15 final size:15
Alignment explanation
Indices: 6698832--6698880 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
6698822 ATAATGCTTA
*
6698832 TAATTACATTACTTG
1 TAATTAAATTACTTG
*
6698847 TAATTATATTACTTG
1 TAATTAAATTACTTG
*
6698862 TAATAAAATTACATTG
1 TAATTAAATTAC-TTG
6698878 TAA
1 TAA
6698881 AGTATCAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 24 0.80
16 6 0.20
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (15 bp):
TAATTAAATTACTTG
Found at i:6699391 original size:11 final size:11
Alignment explanation
Indices: 6699375--6699405 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
6699365 TAAATTCTTA
6699375 TAATTAATTAT
1 TAATTAATTAT
6699386 TAATTAATTAT
1 TAATTAATTAT
6699397 T-ATTAATTA
1 TAATTAATTA
6699406 AAATATCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.40
11 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TAATTAATTAT
Found at i:6700839 original size:235 final size:235
Alignment explanation
Indices: 6700403--6700840 Score: 506
Period size: 235 Copynumber: 1.9 Consensus size: 235
6700393 TTTTAATGTA
* *
6700403 TATTATTTTTTAACAACGATTATTTGAGTTAATAGGCATCAGAGTATAGAGTTTGGATTCATCCC
1 TATTATATTTTAACAACGATTATTTGAGTTAACAGGCATCAGAGTATAGAGTTTGGATTCATCCC
* * * * * * * *
6700468 AACGCTTCGGTGAAAATCCGTATTGAATTCCACTCTTGATAAATCCACCCGAAAGAGGCAACTCT
66 AACACTTCGATAAAAATCCGTATCGAACTCCACTCTTAAGAAATCCACCCGAAAGAAGCAACTCT
* * ** *
6700533 TTACCCATTTGTAGGTGAAATTCTATCCTCGGATCACTCAAAATAATTATTTCATTATTATTATT
131 TTACCCATTTGTAGGTGAAATCCTATCATCGGATCACTCAAAATAACCATTTCATTATTATTATA
6700598 ATTTTATAATAACTATATTTATATCATGTATTTTATTATT
196 ATTTTATAATAACTATATTTATATCATGTATTTTATTATT
* * * * * * * *
6700638 TATTATATTTTGACAATGATTATTTGAGTTAACGGGTATTAGAGTTTAGAGTTTGGATTTATCTC
1 TATTATATTTTAACAACGATTATTTGAGTTAACAGGCATCAGAGTATAGAGTTTGGATTCATCCC
* * * *
6700703 GACACTTCGATAAAAATCCGTCTCGAACTCCGCATC-TAAGAAATCCACCCGAAAGAAGTAACTC
66 AACACTTCGATAAAAATCCGTATCGAACTCCAC-TCTTAAGAAATCCACCCGAAAGAAGCAACTC
* * * * * * *
6700767 TTTGCCTC-TTTTTAGGT-AAAGTCCTATCATCGGATTACTTAAAATAGCCATCTT-ATTTTTTT
130 TTTACC-CATTTGTAGGTGAAA-TCCTATCATCGGATCACTCAAAATAACCAT-TTCATTATTAT
6700829 TATAATTTTATA
192 TATAATTTTATA
6700841 TTTTTATCAT
Statistics
Matches: 165, Mismatches: 34, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
234 3 0.02
235 157 0.95
236 5 0.03
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.39
Consensus pattern (235 bp):
TATTATATTTTAACAACGATTATTTGAGTTAACAGGCATCAGAGTATAGAGTTTGGATTCATCCC
AACACTTCGATAAAAATCCGTATCGAACTCCACTCTTAAGAAATCCACCCGAAAGAAGCAACTCT
TTACCCATTTGTAGGTGAAATCCTATCATCGGATCACTCAAAATAACCATTTCATTATTATTATA
ATTTTATAATAACTATATTTATATCATGTATTTTATTATT
Found at i:6700858 original size:16 final size:16
Alignment explanation
Indices: 6700839--6700879 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
6700829 TATAATTTTA
*
6700839 TATTTTTATCATGTAT
1 TATTTTTATCATATAT
*
6700855 TATTTTTATTATATAT
1 TATTTTTATCATATAT
*
6700871 TATATTTAT
1 TATTTTTAT
6700880 AAGTATTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (16 bp):
TATTTTTATCATATAT
Found at i:6701543 original size:12 final size:11
Alignment explanation
Indices: 6701532--6701583 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
6701522 CTTCTATCCT
6701532 TTTTTCTTTCC
1 TTTTTCTTTCC
6701543 TTTTTCTTT-C
1 TTTTTCTTTCC
*
6701553 --TTTCTCTCC
1 TTTTTCTTTCC
*
6701562 TTTCTTCTATCC
1 TTT-TTCTTTCC
6701574 TTTTTCTTTC
1 TTTTTCTTTC
6701584 TTCTCTCTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
8 6 0.18
9 1 0.03
10 1 0.03
11 16 0.47
12 10 0.29
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTCTTTCC
Found at i:6701562 original size:19 final size:19
Alignment explanation
Indices: 6701530--6701569 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
6701520 CTCTTCTATC
*
6701530 CTTTTTTCTTTCCTTT-TT
1 CTTTTTTCTCTCCTTTCTT
6701548 CTTTCTTTCTCTCCTTTCTT
1 CTTT-TTTCTCTCCTTTCTT
6701568 CT
1 CT
6701570 ATCCTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 11 0.58
20 4 0.21
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
CTTTTTTCTCTCCTTTCTT
Found at i:6701563 original size:31 final size:30
Alignment explanation
Indices: 6701521--6701600 Score: 117
Period size: 31 Copynumber: 2.7 Consensus size: 30
6701511 AACCCCGATC
*
6701521 TCTTCTATCCTTTTTTCTTTCCTTTTTCTT
1 TCTTCTCTCCTTTTTTCTTTCCTTTTTCTT
* *
6701551 TCTTTCTCTCCTTTCTTCTATCCTTTTTCTT
1 TC-TTCTCTCCTTTTTTCTTTCCTTTTTCTT
6701582 TCTTCTCT-CTTTTTTCTTT
1 TCTTCTCTCCTTTTTTCTTT
6701601 TCAGTGGCCG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
29 9 0.20
30 8 0.18
31 27 0.61
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.69
Consensus pattern (30 bp):
TCTTCTCTCCTTTTTTCTTTCCTTTTTCTT
Found at i:6701584 original size:18 final size:18
Alignment explanation
Indices: 6701561--6701600 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
6701551 TCTTTCTCTC
6701561 CTTTCTTCTATCCTTTTT
1 CTTTCTTCTATCCTTTTT
* *
6701579 CTTTCTTCTCTCTTTTTT
1 CTTTCTTCTATCCTTTTT
6701597 CTTT
1 CTTT
6701601 TCAGTGGCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.70
Consensus pattern (18 bp):
CTTTCTTCTATCCTTTTT
Found at i:6702356 original size:30 final size:30
Alignment explanation
Indices: 6702322--6702385 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
6702312 ATTATAAGAG
6702322 TTTATTTAATTTAAAATAAAAATATAAAAA
1 TTTATTTAATTTAAAATAAAAATATAAAAA
*
6702352 TTTATTTAATTTAAAATAAAAATATAAAAT
1 TTTATTTAATTTAAAATAAAAATATAAAAA
6702382 TTTA
1 TTTA
6702386 ATCAAATATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
TTTATTTAATTTAAAATAAAAATATAAAAA
Found at i:6702394 original size:18 final size:19
Alignment explanation
Indices: 6702371--6702406 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
6702361 TTTAAAATAA
6702371 AAATA-TAAAATTTTAATC
1 AAATATTAAAATTTTAATC
6702389 AAATATTAAAATTTTAAT
1 AAATATTAAAATTTTAAT
6702407 TTTTTTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATATTAAAATTTTAATC
Found at i:6726560 original size:43 final size:43
Alignment explanation
Indices: 6726512--6726597 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
6726502 GCAATCGAAA
6726512 GACATCCTAATCCTATTATGACGGCAACATCAGGCTAGAAAAG
1 GACATCCTAATCCTATTATGACGGCAACATCAGGCTAGAAAAG
*
6726555 GACATCCTAATCCTTTTATGACGGCAACATCAGGCTAGAAAAG
1 GACATCCTAATCCTATTATGACGGCAACATCAGGCTAGAAAAG
6726598 TTTGTGGTGG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (43 bp):
GACATCCTAATCCTATTATGACGGCAACATCAGGCTAGAAAAG
Found at i:6729450 original size:70 final size:70
Alignment explanation
Indices: 6729332--6729473 Score: 257
Period size: 70 Copynumber: 2.0 Consensus size: 70
6729322 TAAAATAAAC
*
6729332 TACTTACCCCAGGAATTTGAGTCAAGCTGACTGATTCGACCTCAGAACAAAAACAGACTAAGACA
1 TACTTACCCCAAGAATTTGAGTCAAGCTGACTGATTCGACCTCAGAACAAAAACAGACTAAGACA
6729397 TACAT
66 TACAT
* *
6729402 TACTTACCCCAAGAATTTGAGTCAAGCTGACTGATTCGACCTCGGAACAAAAACAGCCTAAGACA
1 TACTTACCCCAAGAATTTGAGTCAAGCTGACTGATTCGACCTCAGAACAAAAACAGACTAAGACA
6729467 TACAT
66 TACAT
6729472 TA
1 TA
6729474 AGCAGCTAGG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.22
Consensus pattern (70 bp):
TACTTACCCCAAGAATTTGAGTCAAGCTGACTGATTCGACCTCAGAACAAAAACAGACTAAGACA
TACAT
Found at i:6743810 original size:20 final size:20
Alignment explanation
Indices: 6743785--6743825 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
6743775 TTTCTGGTAA
*
6743785 TGTGTCTACTTAAACTAAAT
1 TGTGTCTAATTAAACTAAAT
*
6743805 TGTGTCTAATTAAATTAAAT
1 TGTGTCTAATTAAACTAAAT
6743825 T
1 T
6743826 ATTTATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.44
Consensus pattern (20 bp):
TGTGTCTAATTAAACTAAAT
Found at i:6744190 original size:21 final size:21
Alignment explanation
Indices: 6744141--6744191 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
6744131 TTTACCTTTG
6744141 ATTAATTTTTAAAATTATTATT
1 ATTAA-TTTTAAAATTATTATT
* * *
6744163 ATATAATTTTAAATTTTTTTTT
1 AT-TAATTTTAAAATTATTATT
6744185 ATTAATT
1 ATTAATT
6744192 AAAAAAATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 5 0.20
22 17 0.68
23 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTAATTTTAAAATTATTATT
Found at i:6744832 original size:31 final size:30
Alignment explanation
Indices: 6744777--6744836 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
6744767 CATCTTTTTT
6744777 ATATTTAATTATTATTTTACTTATATATCAA
1 ATATTTAATTATTATTTTACTTATA-ATCAA
**
6744808 ATATTATAA-TATTATTTTTTTTATAATCA
1 ATATT-TAATTATTATTTTACTTATAATCA
6744837 TATTATTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 4 0.15
31 19 0.73
32 3 0.12
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (30 bp):
ATATTTAATTATTATTTTACTTATAATCAA
Found at i:6777699 original size:49 final size:49
Alignment explanation
Indices: 6777644--6777742 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
6777634 ATGTTGTCTC
* *
6777644 TGTAGGTTGAATACCACTTATAACCCTTTGATCAAATTGTTCAAGTGAT
1 TGTAGGTTGAATACCACTTATAACCATTTGATCAAATAGTTCAAGTGAT
6777693 TGTAGGTTGAATACCACTTATAACCATTTGATCAAATAGTTCAAGTGAT
1 TGTAGGTTGAATACCACTTATAACCATTTGATCAAATAGTTCAAGTGAT
6777742 T
1 T
6777743 TCCTTACATC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Consensus pattern (49 bp):
TGTAGGTTGAATACCACTTATAACCATTTGATCAAATAGTTCAAGTGAT
Found at i:6778758 original size:45 final size:45
Alignment explanation
Indices: 6778694--6778819 Score: 144
Period size: 45 Copynumber: 2.8 Consensus size: 45
6778684 CGTTATGATA
* * * * * *
6778694 TTACAAATCATGTACAAAAATATGTTATACGTCATGATTAGGTTG
1 TTACACATCATGTACAAAAACACGTGACACATCATGATTAGGTTG
* *
6778739 TTACACGTCATGTGCAAAAACACGTGACACATCATGATTAGGTTG
1 TTACACATCATGTACAAAAACACGTGACACATCATGATTAGGTTG
* ** *
6778784 TTACATATCATGTACAAAAACATATGACACAACATG
1 TTACACATCATGTACAAAAACACGTGACACATCATG
6778820 TACAGAAACA
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 67 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (45 bp):
TTACACATCATGTACAAAAACACGTGACACATCATGATTAGGTTG
Found at i:6778856 original size:24 final size:24
Alignment explanation
Indices: 6778792--6778862 Score: 88
Period size: 24 Copynumber: 3.0 Consensus size: 24
6778782 TGTTACATAT
* * *
6778792 CATGTACAAAAACATATGACACAA
1 CATGTACAAAAACATGTGATACGA
* *
6778816 CATGTACAGAAACATGTGATACGC
1 CATGTACAAAAACATGTGATACGA
*
6778840 CATGTACAAAAATATGTGATACG
1 CATGTACAAAAACATGTGATACG
6778863 TCATAATTAG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.45, C:0.18, G:0.15, T:0.21
Consensus pattern (24 bp):
CATGTACAAAAACATGTGATACGA
Found at i:6778913 original size:30 final size:29
Alignment explanation
Indices: 6778874--6779050 Score: 124
Period size: 29 Copynumber: 6.3 Consensus size: 29
6778864 CATAATTAGA
6778874 TTGTTACACGTCATGTTGAAAAAAATATTG
1 TTGTTACACGTCATGTT-AAAAAAATATTG
* * *
6778904 TTATTACACGTCATG-TACAAAAACA---
1 TTGTTACACGTCATGTTAAAAAAATATTG
*
6778929 -TGTTACACGTCATGGTT--AAAAA-A-GG
1 TTGTTACACGTCAT-GTTAAAAAAATATTG
* * *
6778954 TTGTTACACATCATATTGAAAAAAAAATACTG
1 TTGTTACACGTCATGTT---AAAAAAATATTG
* * *
6778986 TTGTTATACGTCATGTTAAAGAAATATTA
1 TTGTTACACGTCATGTTAAAAAAATATTG
* *
6779015 TTGTTACACGTCATATT-CAAAAATATT-
1 TTGTTACACGTCATGTTAAAAAAATATTG
6779042 TTGTTACAC
1 TTGTTACAC
6779051 TTTAATGTCT
Statistics
Matches: 118, Mismatches: 17, Indels: 27
0.73 0.10 0.17
Matches are distributed among these distances:
23 1 0.01
24 17 0.14
25 3 0.03
26 13 0.11
27 9 0.08
28 15 0.13
29 25 0.21
30 19 0.16
31 1 0.01
32 15 0.13
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (29 bp):
TTGTTACACGTCATGTTAAAAAAATATTG
Found at i:6779064 original size:28 final size:28
Alignment explanation
Indices: 6778976--6779076 Score: 89
Period size: 29 Copynumber: 3.6 Consensus size: 28
6778966 ATATTGAAAA
* * * * *
6778976 AAAAATACTGTTGTTATACGTCATGTTA
1 AAAAATATTATTGTTACACGTCATATTC
6779004 AAGAAATATTATTGTTACACGTCATATTC
1 AA-AAATATTATTGTTACACGTCATATTC
* *
6779033 AAAAATATT-TTGTTACACTTTA-ATGTC
1 AAAAATATTATTGTTACACGTCATAT-TC
* *
6779060 TAAAATGTTATTGTTAC
1 AAAAATATTATTGTTAC
6779077 TTACGAACCA
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
26 2 0.03
27 20 0.33
28 16 0.26
29 23 0.38
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (28 bp):
AAAAATATTATTGTTACACGTCATATTC
Found at i:6780048 original size:2 final size:2
Alignment explanation
Indices: 6780041--6780088 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
6780031 GAAAATCACN
6780041 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6780083 TA TA TA
1 TA TA TA
6780089 ATTAGGAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6785264 original size:22 final size:23
Alignment explanation
Indices: 6785236--6785282 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
6785226 ATTTTTTTGC
6785236 ATTACTA-CAAGAACTAAGCT-AA
1 ATTACTATCAA-AACTAAGCTCAA
*
6785258 ATTACTATCAAAATTAAGCTCAA
1 ATTACTATCAAAACTAAGCTCAA
6785281 AT
1 AT
6785283 AACTCTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.28
Consensus pattern (23 bp):
ATTACTATCAAAACTAAGCTCAA
Found at i:6787703 original size:28 final size:29
Alignment explanation
Indices: 6787654--6787722 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 29
6787644 TACCCACATG
*
6787654 TTATACTCATCTAAGTGCCAAACAT-TGCA
1 TTATA-TCATTTAAGTGCCAAACATATGCA
* * *
6787683 TTATATCATTTATGTGTCAAATATATGCA
1 TTATATCATTTAAGTGCCAAACATATGCA
* *
6787712 TAATATTATTT
1 TTATATCATTT
6787723 TAGGTCTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 15 0.45
29 18 0.55
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (29 bp):
TTATATCATTTAAGTGCCAAACATATGCA
Found at i:6790757 original size:14 final size:15
Alignment explanation
Indices: 6790738--6790766 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6790728 GTTTTGATTG
6790738 CTTTTT-CTTTTTTT
1 CTTTTTCCTTTTTTT
6790752 CTTTTTCCTTTTTTT
1 CTTTTTCCTTTTTTT
6790767 TTTGGCTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
CTTTTTCCTTTTTTT
Found at i:6818596 original size:26 final size:25
Alignment explanation
Indices: 6818567--6818813 Score: 145
Period size: 26 Copynumber: 10.4 Consensus size: 25
6818557 TTCATTAAAA
6818567 ATTGCGTGACTAGTTTCTGATAAGGC
1 ATTGCGTGACTAGTTT-TGATAAGGC
* *
6818593 ATTGTGTGACTAG--TTAATAA-GC
1 ATTGCGTGACTAGTTTTGATAAGGC
* * *
6818615 ATTGGGTGACT-GACTTTG---A-GT
1 ATTGCGTGACTAG-TTTTGATAAGGC
* *
6818636 ATTGCGTAACTAGTTTTTTATAAGGC
1 ATTGCGTGACTAG-TTTTGATAAGGC
* *
6818662 ATTGCGTGACTAGTTTCTGATAAAGT
1 ATTGCGTGACTAGTTT-TGATAAGGC
* **
6818688 ATTGTGTGACTAACTTTG----GGC
1 ATTGCGTGACTAGTTTTGATAAGGC
*
6818709 ATTGCGTGACTAGTTTCTGATAAGGG
1 ATTGCGTGACTAGTTT-TGATAAGGC
*
6818735 ATTGCATGACTAG--TTGAT-AGGC
1 ATTGCGTGACTAGTTTTGATAAGGC
* *
6818757 ATTGCGTGACTTG-TTAG-TAAGGC
1 ATTGCGTGACTAGTTTTGATAAGGC
* *
6818780 ATTGCGTGACTA--ATTCATAAGGC
1 ATTGCGTGACTAGTTTTGATAAGGC
*
6818803 ATTGTGTGACT
1 ATTGCGTGACT
6818814 TAGGCATTGC
Statistics
Matches: 170, Mismatches: 34, Indels: 37
0.71 0.14 0.15
Matches are distributed among these distances:
21 26 0.15
22 34 0.20
23 42 0.25
24 4 0.02
25 6 0.04
26 58 0.34
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.36
Consensus pattern (25 bp):
ATTGCGTGACTAGTTTTGATAAGGC
Found at i:6818723 original size:73 final size:71
Alignment explanation
Indices: 6818567--6818749 Score: 226
Period size: 73 Copynumber: 2.6 Consensus size: 71
6818557 TTCATTAAAA
* *
6818567 ATTGCGTGACTAGTTTCTGATAAGGCATTGTGTGACTAG--TTAATAAGCATTGGGTGACTGACT
1 ATTGCGTGACTAGTTTCTGATAAGGCATTGCGTGACTAGTTTTAATAAGCATTGGGTGACTAACT
*
6818630 TTGAGT
66 TTGAGC
* * * * * *
6818636 ATTGCGTAACTAGTTTTTTATAAGGCATTGCGTGACTAGTTTCTGATAAAGTATTGTGTGACTAA
1 ATTGCGTGACTAGTTTCTGATAAGGCATTGCGTGACTAGTTT-TAAT-AAGCATTGGGTGACTAA
*
6818701 CTTTGGGC
64 CTTTGAGC
* *
6818709 ATTGCGTGACTAGTTTCTGATAAGGGATTGCATGACTAGTT
1 ATTGCGTGACTAGTTTCTGATAAGGCATTGCGTGACTAGTT
6818750 GATAGGCATT
Statistics
Matches: 95, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
69 35 0.37
71 1 0.01
72 3 0.03
73 56 0.59
ACGTcount: A:0.25, C:0.12, G:0.26, T:0.38
Consensus pattern (71 bp):
ATTGCGTGACTAGTTTCTGATAAGGCATTGCGTGACTAGTTTTAATAAGCATTGGGTGACTAACT
TTGAGC
Found at i:6818783 original size:23 final size:23
Alignment explanation
Indices: 6818706--6818815 Score: 84
Period size: 23 Copynumber: 4.7 Consensus size: 23
6818696 ACTAACTTTG
6818706 GGCATTGCGTGAC-TAGTTTCTGATAA
1 GGCATTGCGTGACTTA--TTC--ATAA
* * *
6818732 GGGATTGCATGAC-TAGTTGAT-A
1 GGCATTGCGTGACTTA-TTCATAA
*
6818754 GGCATTGCGTGACTTGTT-AGTAA
1 GGCATTGCGTGACTTATTCA-TAA
*
6818777 GGCATTGCGTGACTAATTCATAA
1 GGCATTGCGTGACTTATTCATAA
*
6818800 GGCATTGTGTGACTTA
1 GGCATTGCGTGACTTA
6818816 GGCATTGCTT
Statistics
Matches: 69, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
21 1 0.01
22 15 0.22
23 37 0.54
24 1 0.01
25 2 0.03
26 13 0.19
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.34
Consensus pattern (23 bp):
GGCATTGCGTGACTTATTCATAA
Done.